Carbohydrate sensors

ABSTRACT

The present invention relates to sensors and methods for detecting carbohydrates, such as lactose, in a sample. The sensors and methods may also be used to determine the amount of carbohydrate in the sample.

FIELD OF THE INVENTION

The present invention relates to sensors and methods for detecting carbohydrates, such as lactose, in a sample. The sensors and methods may also be used to determine the amount of carbohydrate in the sample.

BACKGROUND OF THE INVENTION

Assays for detecting carbohydrates, including sugars and sugar derivatives, are widely used in the food and medical industries. Of particular interest to the food industry are assays for detecting carbohydrates, such as lactose, in dairy products.

Currently, routine lactose analysis in dairy products is achieved with high-performance liquid chromatography (HPLC). This method yields accurate, sensitive and selective measurement of lactose but the analysis requires transport of samples to a laboratory facility with expensive apparatus operated by highly trained staff (Euber and Brunner, 1979; Indyk et al., 1996; Xinmin et al., 2008; Erich et al., 2012). Other technologies for detecting/measuring lactose use enzymatic cascades to indirectly measure the concentration of lactose in solution. These assays normally proceed through enzymatic hydrolysis of lactose to galactose and glucose with β-galactosidase, followed by oxidation of either of the monosaccharides (Kleyn, 1985; Ansari et al., 2012; Jia et al., 2014). Quantification of lactose is achieved through the measurement of the stoichiometric bi-products of the oxidation step, namely NADH or H₂O₂, using spectrophotometric, amperometric or colorimetric methods. These assays require a number of reagents and numerous steps making them too lengthy and cumbersome for routine use in a processing plant. They have inherently low selectivity. Alternatively, high levels of lactose (e.g. 3.9-4.8% (w/v)) may be measured by near infrared spectroscopy (Tsenkova et al., 1999). However, this method is inaccurate for measuring lower levels of lactose, such as below 1% (w/v) lactose, and requires expensive equipment.

Accordingly, there is a need for further methods of detecting and quantifying the amount of carbohydrates in a sample, preferably methods that can be performed in real time, with increased sensitivity and/or without having to send samples offsite for analysis.

SUMMARY OF THE INVENTION

The present inventors have identified sensors that can be used to detect carbohydrates in a sample. The present inventors have also identified an improved method of detecting the presence of carbohydrates in a sample using these sensors. In some embodiments, these sensors and methods can be used measure the concentration of carbohydrate in a sample. They have also identified an improved method of detecting lactose of a dairy product using these sensors. In some embodiments, the sensors and methods can be used to measure the lactose content of a dairy product. In some embodiments, the sensors and methods can be used to classify dairy products based on their lactose content.

In one aspect, there is provided a sensor molecule for detecting a carbohydrate, the sensor comprising:

i) a carbohydrate binding domain of a helix-turn-helix transcription factor, or a variant of the carbohydrate binding domain;

ii) a chemiluminescent donor domain; and

iii) an acceptor domain;

wherein the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain is altered when the carbohydrate binds to the carbohydrate binding domain.

In some embodiments, the helix-turn-helix transcription factor is a bacterial helix-turn-helix transcription factor, or a variant thereof. In some embodiments, the bacterial helix-turn-helix transcription factor is a G_(NT)R transcription factor, or a variant thereof. In some embodiments, the bacterial helix-turn-helix transcription factor or variant thereof, has an amino acid sequence which is at least 60% identical to that provided in SEQ ID NO: 1. In another embodiment, the binding domain has an amino acid sequence which is at least 60% identical to that provided in SEQ ID NO: 9.

In a further embodiment, the binding domain has an amino acid sequence which is at least 30% identical to that provided in any one or more of SEQ ID NO's 9 and 56 to 74.

In some embodiments, the carbohydrate is a sugar or sugar derivative. In some embodiments, the carbohydrate is a sugar. In some embodiments, the sugar is a disaccharide. In preferred embodiments, the disaccharide is lactose. In another embodiment, the disaccharide is lactulose. In some embodiments, the carbohydrate is a sugar derivative. In some embodiments, the sugar derivative is selected from the group consisting of amino sugars, acidic sugars, deoxy sugars, sugar alcohols, glycosylamines and sugar phosphates.

In some embodiments, the chemiluminescent donor domain is a bioluminescent protein. In some embodiments, the bioluminescent protein is a luciferase, a β-galactosidase, a lactamase, a horseradish peroxidase, an alkaline phosphatase, a β-glucuronidase or a β-glucosidase. In some embodiments, the bioluminescent protein is a luciferase. In some embodiments, the luciferase is a Renilla luciferase, a Firefly luciferase, a Coelenterate luciferase, a North American glow worm luciferase, a click beetle luciferase, a railroad worm luciferase, a bacterial luciferase, a Gaussia luciferase, Aequorin, an Arachnocampa luciferase, an Oplophorus gracilirostris luciferase or a biologically active variant or fragment of any one, or chimera of two or more, thereof.

In some embodiments, the chemiluminescent donor domain is capable of modifying a substrate. In some embodiments, the substrate is luciferin, calcium, coelenterazine, furimazine or a derivative, analogue or stabilised derivative of coelenterazine, luciferin or furimazine.

In some embodiments, the acceptor domain is a fluorescent acceptor domain. In some embodiments, the fluorescent acceptor domain is selected from the group consisting of green fluorescent protein (GFP), blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Venus, mOrange, Topaz, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), HcRed, t-HcRed, DsRed, DsRed2, t-dimer2, tdimer2(12), mRFP1, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein, tdTomato, mCherry, TagRFP, TurBoFB and a Phycobiliprotein, and a biologically active variant or fragment of any one thereof.

In some embodiments, the separation and relative orientation of the chemiluminescent donor domain and the acceptor domain, in the presence and/or the absence of carbohydrate, is within ±50% of the Förster distance. In some embodiments, the Förster distance of the chemiluminescent donor domain and the acceptor domain is at least 5.6 nm. In some embodiments, the Förster distance of the chemiluminescent donor domain and the acceptor domain is between about 7 nm and about 11 nm.

In another aspect there is also provided a method of detecting a carbohydrate in a sample, the method comprising

i) contacting a sample with the sensor molecule defined herein; and

ii) determining if the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain has been altered in the presence of the sample,

wherein an alteration of the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain indicates the carbohydrate is present in the sample.

In some embodiments, the method further comprises determining the concentration of the carbohydrate in the sample. In some embodiments, the method is performed on a microfluidic device. In some embodiments, the sample is air, liquid, biological material or soil. In some embodiments, the sample comprises a dairy product. In preferred embodiments, the sample is milk.

In yet another aspect there is provided a sensor molecule for detecting lactose comprising a bacterial BgaR transcription factor or variant thereof, covalently joined to a resonance energy transfer donor domain and a resonance energy transfer acceptor domain, wherein the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain is altered when lactose binds to the transcription factor.

Binding of lactose to the sensor molecule produces a change in resonance energy transfer (RET), for example a change in BRET or a change in FRET. Accordingly, the sensors can be used to detect the presence of lactose in a sample and/or to determine the concentration of lactose in a sample.

In yet another aspect there is provided a sensor molecule for detecting lactulose comprising a bacterial BgaR transcription factor or variant thereof, covalently joined to a resonance energy transfer donor domain and a resonance energy transfer acceptor domain, wherein the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain is altered when lactulose binds to the transcription factor. Binding of lactulose to the sensor molecule produces a change in resonance energy transfer (RET), for example a change in BRET or a change in FRET. Accordingly, the sensors can be used to detect the presence of lactulose in a sample and/or to determine the concentration of lactose in a sample.

In some embodiments, the transcription factor or variant thereof, has an amino acid sequence which is at least 60%, 70%, 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to that provided in SEQ ID NO: 1. In some embodiments, the transcription factor or variant thereof, has the amino acid sequence provided in SEQ ID NO: 1.

The sensor molecule can be a BRET or FRET based sensor. In some embodiments, the sensor molecule is a BRET based sensor such that binding of lactose to the sensor molecule produces a change in BRET. Accordingly, in some embodiments, the resonance energy transfer donor domain is a bioluminescent protein. Suitable bioluminescent proteins include a luciferase, a β-galactosidase, a lactamase, a horseradish peroxidase, an alkaline phosphatase, a β-glucuronidase or a β-glucosidase. In some embodiments, the bioluminescent protein is a luciferase. In some embodiments, luciferase is a Renilla luciferase, a Firefly luciferase, a Coelenterate luciferase, a North American glow worm luciferase, a click beetle luciferase, a railroad worm luciferase, a bacterial luciferase, a Gaussia luciferase, Aequorin, an Arachnocampa luciferase, an Oplophorus gracilirostris luciferase or a biologically active variant or fragment of any one, or chimera of two or more, thereof. In some embodiments, the donor domain is capable of modifying a substrate. Suitable substrates include luciferin, calcium, coelenterazine, furimazine or a derivative, analogue or stabilised derivative of coelenterazine, luciferin or furimazine.

In some embodiments, the sensor molecule is a FRET based sensor such that binding of lactose to the sensor molecule produces a change in FRET. Accordingly, in some embodiments, the resonance energy transfer donor domain is a fluorescent protein. In some embodiments, the fluorescent protein is selected from the group consisting of green fluorescent protein (GFP), blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Venus, mOrange, Topaz, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), HcRed, t-HcRed, DsRed, DsRed2, t-dimer2, tdimer2(12), mRFP1, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein, tdTomato, mCherry, TagRFP, TurBoFB and a Phycobiliprotein, and a biologically active variant or fragment of any one thereof.

For both BRET and FRET based lactose sensors, the resonance energy transfer acceptor domain can be a fluorescent acceptor domain. In some embodiments, the fluorescent acceptor domain is a fluorescent protein. In some embodiments, the fluorescent acceptor domain is selected from the group consisting of green fluorescent protein (GFP), blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Venus, mOrange, Topaz, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), HcRed, t-HcRed, DsRed, DsRed2, t-dimer2, tdimer2(12), mRFP1, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein, tdTomato, mCherry, TagRFP, TurBoFB and a Phycobiliprotein, and a biologically active variant or fragment of any one thereof.

In some embodiments, the resonance energy transfer donor domain is Renilla luciferase or a variant thereof and the resonance energy transfer acceptor domain is GFP or a variant thereof. In some embodiments, the present disclosure provides a sensor molecule having at least 60%, 70%, 80%, 85%, 90%, 95%, 98%, 99% or 100% sequence identity to a polypeptide sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18. In these embodiments, binding of lactose to the sensor molecule produces a change in BRET.

In some embodiments, the resonance energy transfer donor domain is CFP or a variant thereof and the resonance energy transfer acceptor domain is YFP or a variant thereof. In some embodiments, the present disclosure provides a sensor molecule having at least 60%, 70%, 80%, 85%, 90%, 95%, 98%, 99% or 100% sequence identity to the polypeptide provided in SEQ ID NO: 23. In these embodiments, binding of lactose to the sensor molecule produces a change in FRET.

In some embodiments, the separation and relative orientation of the donor domain and the acceptor domain, in the presence and/or the absence of lactose, is within ±50% of the Förster distance. In some embodiments, the Förster distance of the donor domain and the acceptor domain is at least 5.6 nm. In some embodiments, the Förster distance of the donor domain and the acceptor domain is between about 5.6 nm and about 10 nm.

In another aspect there is also provided a method of detecting lactose in a sample, the method comprising

i) contacting a sample with the sensor molecule for detecting lactose as defined herein; and

ii) determining if the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain has been altered in the presence of the sample,

wherein an alteration of the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain indicates that lactose is present in the sample. In some embodiments, the method further comprises determining the concentration of lactose in the sample. In some embodiments, the method is performed on a microfluidic device. In some embodiments, the sample is air, liquid, biological material or soil. In some embodiments, the sample comprises a dairy product. In some embodiments, the dairy product is milk.

In another aspect there is also provided a method of detecting lactulose in a sample, the method comprising

i) contacting a sample with the sensor molecule as defined herein; and

ii) determining if the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain has been altered in the presence of the sample,

wherein an alteration of the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain indicates that lactulose is present in the sample. In some embodiments, the method further comprises determining the concentration of lactulose in the sample. In some embodiments, the method is performed on a microfluidic device. In some embodiments, the sample is air, liquid, biological material or soil. In some embodiments, the sample comprises a dairy product. In some embodiments, the dairy product is milk.

In some embodiments, the sensor molecule is a single polypeptide. In some embodiments, the chemiluminescent donor domain is at the N-terminus and the acceptor domain is at the C-terminus. In alternative embodiments, the acceptor domain is at the N-terminus and the chemiluminescent donor domain is at the C-terminus. In some embodiments, the resonance energy transfer donor domain is at the N-terminus and the resonance energy transfer acceptor domain is at the C-terminus. In alternative embodiments, the resonance energy transfer acceptor domain is at the N-terminus and the resonance energy transfer donor domain is at the C-terminus.

In some embodiments, the sensor molecule comprises at least one peptide linker.

In another aspect there is also provided a polynucleotide encoding a sensor molecule as defined herein. In another aspect there is also provided a vector comprising a polynucleotide encoding a sensor molecule as defined herein. In yet another aspect there is also provided a host cell comprising the polynucleotide and/or the vector defined herein. In yet another aspect there is also provided a process for producing a sensor molecule, the process comprising cultivating a host cell or a vector defined herein under conditions which allow expression of the polynucleotide encoding the polypeptide, and recovering the expressed polypeptide.

Any embodiment herein shall be taken to apply mutatis mutandis to any other embodiment unless specifically stated otherwise.

The present invention is not to be limited in scope by the specific embodiments described herein, which are intended for the purpose of exemplification only. Functionally-equivalent products, compositions and methods are clearly within the scope of the invention, as described herein.

Throughout this specification, unless specifically stated otherwise or the context requires otherwise, reference to a single step, composition of matter, group of steps or group of compositions of matter shall be taken to encompass one and a plurality (i.e. one or more) of those steps, compositions of matter, groups of steps or group of compositions of matter.

The invention is hereinafter described by way of the following non-limiting Examples and with reference to the accompanying figures.

BRIEF DESCRIPTION OF THE ACCOMPANYING DRAWINGS

FIG. 1—Schematic representation of an embodiment of the present disclosure. The illustrated sensor molecule, LacB1, comprises the BgaR transcriptional factor flanked with GFP² and RLuc8 at the N- and C-terminus, respectively.

FIG. 2—RET ratios (means±SD, n=3) for 1 μM of LacB1 and LacF1 sensors in water (dark grey bars) or 1 mM lactose (light grey bars). BRET² scans were recorded following the addition of 17 μM coelenterazine 400a substrate. *P<0.0001.

FIG. 3—BRET² response of LacB1 to 0.000034 w/v %-0.34% w/v of lactose.

FIG. 4—Schematic representation of an embodiment of the present disclosure. LacB1 comprises the BgaR transcriptional factor (light grey) flanked with GFP² (mid grey) and RLuc8 (dark grey) at the N- and C-terminus, respectively. LacB2 comprises LacB1 with the amino acid linker -GGTGGG- inserted between BgaR and GFP² and BgaR and RLuc8. LacB3 comprises LacB1 with the linker -GGTGGG- inserted between BgaR and GFP². LacB4 comprises LacB1 with the linker -GGTGGG- inserted between BgaR and RLuc8. The location of the linker is represented by the black section joining BgaR and GFP² and/or BgaR and RLuc8.

FIG. 5—BRET² response of LacB1 (1), LacB2 (2), LacB3 (3) and LacB4 (4) to the presence of 1 mM lactose.

FIG. 6—Changes in BRET² ratio of the LacB1 sensor in the presence of the disaccharides, lactose, maltose and lactulose and the monosaccharides, galactose and glucose. BRET² ratios (mean±SD, n=3) were recorded following addition of 17 μM coelenterazine 400a to 1 μM of LacB1 after incubation with the specified sugars for 30 minutes at 30° C. BRET² ratios were normalized to the water response and expressed as percentages of BRET² change.

FIG. 7—Response of LacB1 to a range of di- and mono-saccharides, all at 1 mM concentrations. BRET² ratios (mean±SD, n=3) were recorded following addition of 17 μM coelenterazine 400a to 1 μM of LacB1 after incubation with the specified sugars for 5 minutes at 30° C. BRET² ratios were normalized to the water response and expressed as percentages of BRET² change.

FIG. 8 —Detection of lactose by the LacB1 sensor in the presence of galactose and glucose in PBS (A) and galactose and glucose in dialysed milk (C, E) (mean±S.D., n=3). Detection of lactose by the LacF1 sensor in the presence of galactose and glucose in PBS (B) and galactose and glucose in dialysed milk (D) (mean±S.D., n=3).

FIG. 9—Detection of lactose and lactulose by the LacB1 sensor in PBS and 10% (v/v) dialysed whole milk supplemented with lactose, galactose and glucose. Solid line: lactose concentration dependence of LacB1 in PBS. EC₅₀=12±1 μM, LOD=1 μM. Dashed line: lactose concentration dependence of LacB1 in 10% dialysed whole milk with lactose, galactose and glucose added such that ([lactose]+[galactose+glucose]/2=13.9 mM). EC₅₀=21±2 μM, LOD=0.2 μM. Dotted line: lactulose concentration dependence of LacB1 in PBS. EC₅₀=2.4±0.2 mM, LOD=0.1 mM.

FIG. 10—(A) Example trace of BRET² ratio for the LacB1 sensor in the presence of 3 mM lactose in assay buffer (0.45% gelatine in phosphate buffer saline), determined using the CYBERTONGUE® device. (B) Example trace of donor emission (upper window, dark grey) and acceptor emission (upper window, light grey) intensities recorded by the CYBERTONGUE® device for LacB1 in the presence of 3 mM lactose in assay buffer.

FIG. 11—Changes in the BRET² ratio of LacB1 determined with the CYBERTONGUE® device. BRET² ratios for LacB1 in the presence of 30 μM and 3 mM lactose were recorded with the CYBERTONGUE® device. The BRET² ratios were normalized to the assay buffer response and expressed as a percentage of BRET² change (mean±S.D., n=2 or 3).

KEY TO THE SEQUENCE LISTING

-   SEQ ID NO: 1—Amino acid sequence of the BgaR HTH transcription     factor. -   SEQ ID NO's: 2 to 8—Linker sequences. -   SEQ ID NO: 9—BgaR HTH carbohydrate binding domain. -   SEQ ID NO's: 10-14—Primer sequences. -   SEQ ID NO: 15—Amino acid sequence of LacB1 (GFP²-BgaR-RLuc8 fusion     protein). -   SEQ ID NO: 16—Amino acid sequence of LacB2 (GFP²-BgaR-RLuc8 fusion     protein). -   SEQ ID NO: 17—Amino acid sequence of LacB3 (GFP²-BgaR-RLuc8 fusion     protein). -   SEQ ID NO: 18—Amino acid sequence of LacB4 (GFP²-BgaR-RLuc8 fusion     protein). -   SEQ ID NO: 19—Nucleotide sequence encoding LacB1 (GFP²-BgaR-RLuc8     fusion protein). -   SEQ ID NO: 20—Nucleotide sequence encoding LacB2 (GFP²-BgaR-RLuc8     fusion protein). -   SEQ ID NO: 21—Nucleotide sequence encoding LacB3 (GFP²-BgaR-RLuc8     fusion protein). -   SEQ ID NO: 22—Nucleotide sequence encoding LacB4 (GFP²-BgaR-RLuc8     fusion protein). -   SEQ ID NO: 23—Amino acid sequence of LacF1 (His₆-CFP-BgaR-YFP fusion     protein). -   SEQ ID NO: 24—Nucleotide sequence encoding LacF1 (His₆-CFP-BgaR-YFP     fusion protein). -   SEQ ID NO: 25—Amino acid sequence of LacB1 (His₆-GFP²-BgaR-RLuc8     fusion protein). -   SEQ ID NO: 26—Amino acid sequence of LacB2 (His₆-GFP²-BgaR-RLuc8     fusion protein). -   SEQ ID NO: 27—Amino acid sequence of LacB3 (His₆-GFP²-BgaR-RLuc8     fusion protein). -   SEQ ID NO: 28—Amino acid sequence of LacB4 (His₆-GFP²-BgaR-RLuc8     fusion protein). -   SEQ ID NO: 29—Nucleotide sequence encoding LacB1     (His₆-GFP²-BgaR-RLuc8 fusion protein). -   SEQ ID NO: 30—Nucleotide sequence encoding LacB2     (His₆-GFP²-BgaR-RLuc8 fusion protein). -   SEQ ID NO: 31—Nucleotide sequence encoding LacB3     (His₆-GFP²-BgaR-RLuc8 fusion protein). -   SEQ ID NO: 32—Nucleotide sequence encoding LacB4     (His₆-GFP²-BgaR-RLuc8 fusion protein). -   SEQ ID NO: 33—Amino acid sequence of LacB1₁₋₁₇₁     (GFP²-BgaR₁₋₁₇₁-RLuc8 fusion protein). A sensor molecule according     to an embodiment of the present disclosure comprising residues 1-171     of BgaR flanked by GFP² and RLuc8. -   SEQ ID NO: 34—Amino acid sequence of LacB₁₋₁₅₀ (GFP²-BgaR₁₋₁₅₀-RLuc8     fusion protein). A sensor molecule according to an embodiment of the     present disclosure comprising residues 1-150 of BgaR flanked by GFP²     and RLuc8. -   SEQ ID NO: 35—Amino acid sequence of LacB1₁₂₋₁₇₁     (GFP²-BgaR₁₂₋₁₇₁-RLuc8 fusion protein). A sensor molecule according     to an embodiment of the present disclosure comprising residues     12-171 of BgaR flanked by GFP² and RLuc8. -   SEQ ID NO: 36—Amino acid sequence of LacB1₁₂₋₁₅₀     (GFP²-BgaR₁₂₋₁₅₀-RLuc8 fusion protein). A sensor molecule according     to an embodiment of the present disclosure comprising residues     12-150 of BgaR flanked by GFP² and RLuc8. -   SEQ ID NO: 37—Amino acid sequence of UniProt Accession No:     A0A133MUX6. -   SEQ ID NO: 38—Amino acid sequence of UniProt Accession No: B1V7N0. -   SEQ ID NO: 39—Amino acid sequence of UniProt Accession No:     A0A127EGD8. -   SEQ ID NO: 40—Amino acid sequence of UniProt Accession No:     A0A1C6JUB7. -   SEQ ID NO: 41—Amino acid sequence of UniProt Accession No:     A0A174HYB7. -   SEQ ID NO: 42—Amino acid sequence of UniProt Accession No:     A0A1C6KY47. -   SEQ ID NO: 43—Amino acid sequence of UniProt Accession No:     A0A174LZQ7. -   SEQ ID NO: 44—Amino acid sequence of UniProt Accession No: N9YR91. -   SEQ ID NO: 45—Amino acid sequence of UniProt Accession No:     A0A174I591. -   SEQ ID NO: 46—Amino acid sequence of UniProt Accession No:     A0A2A7ME67. -   SEQ ID NO: 47—Amino acid sequence of UniProt Accession No:     A0A2K4AZL9. -   SEQ ID NO: 48—Amino acid sequence of UniProt Accession No:     A0A166PPM9. -   SEQ ID NO: 49—Amino acid sequence of UniProt Accession No:     A0A2T4R7G1. -   SEQ ID NO: 50—Amino acid sequence of UniProt Accession No:     A0A2A4HCU9. -   SEQ ID NO: 51—Amino acid sequence of UniProt Accession No:     A0A2T4MS83. -   SEQ ID NO: 52—Amino acid sequence of UniProt Accession No: O33813. -   SEQ ID NO: 53—Amino acid sequence of UniProt Accession No:     A0A1D4LKB2. -   SEQ ID NO: 54—Amino acid sequence of UniProt Accession No:     A0A133QVV5. -   SEQ ID NO: 55—Amino acid sequence of UniProt Accession No: A9QSR3. -   SEQ ID NO: 56—Amino acid sequence of putative carbohydrate binding     domain (CBD) of UniProt Accession No: A0A133MUX6. -   SEQ ID NO: 57—Amino acid sequence of putative CBD of UniProt     Accession No: B1V7N0. -   SEQ ID NO: 58—Amino acid sequence of putative CBD of UniProt     Accession No: A0A127EGD8. -   SEQ ID NO: 59—Amino acid sequence of putative CBD of UniProt     Accession No: A0A1C6JUB7. -   SEQ ID NO: 60—Amino acid sequence of putative CBD of UniProt     Accession No: A0A174HYB7. -   SEQ ID NO: 61—Amino acid sequence of putative CBD of UniProt     Accession No: A0A1C6KY47. -   SEQ ID NO: 62—Amino acid sequence of putative CBD of UniProt     Accession No: A0A174LZQ7. -   SEQ ID NO: 63—Amino acid sequence of putative CBD of UniProt     Accession No: N9YR91. -   SEQ ID NO: 64—Amino acid sequence of putative CBD of UniProt     Accession No: A0A174I591. -   SEQ ID NO: 65—Amino acid sequence of putative CBD of UniProt     Accession No: A0A2A7ME67. -   SEQ ID NO: 66—Amino acid sequence of putative CBD of UniProt     Accession No: A0A2K4AZL9. -   SEQ ID NO: 67—Amino acid sequence of putative CBD of UniProt     Accession No: A0A166PPM9. -   SEQ ID NO: 68—Amino acid sequence of putative CBD of UniProt     Accession No: A0A2T4R7G1. -   SEQ ID NO: 69—Amino acid sequence of putative CBD of UniProt     Accession No: A0A2A4HCU9. -   SEQ ID NO: 70—Amino acid sequence of putative CBD of UniProt     Accession No: A0A2T4MS83. -   SEQ ID NO: 71—Amino acid sequence of putative CBD of UniProt     Accession No: 033813. -   SEQ ID NO: 72—Amino acid sequence of putative CBD of UniProt     Accession No: A0A1D4LKB2. -   SEQ ID NO: 73—Amino acid sequence of putative CBD of UniProt     Accession No: A0A133QVV5. -   SEQ ID NO: 74—Amino acid sequence of putative CBD of UniProt     Accession No: A9QSR3.

DETAILED DESCRIPTION OF THE INVENTION General Techniques and Definitions

Unless specifically defined otherwise, all technical and scientific terms used herein shall be taken to have the same meaning as commonly understood by one of ordinary skill in the art (e.g., in sensor technology, molecular biology, protein chemistry, dairy science, dairy technology, biochemistry and the like).

Unless otherwise indicated, the recombinant protein, cell culture, and immunological techniques utilized in the present invention are standard procedures, well known to those skilled in the art. Such techniques are described and explained throughout the literature in sources such as, J. Perbal, A Practical Guide to Molecular Cloning, John Wiley and Sons (1984), J. Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbour Laboratory Press (1989), T. A. Brown (editor), Essential Molecular Biology: A Practical Approach, Volumes 1 and 2, IRL Press (1991), D. M. Glover and B. D. Hames (editors), DNA Cloning: A Practical Approach, Volumes 1-4, IRL Press (1995 and 1996), and F. M. Ausubel et al., (editors), Current Protocols in Molecular Biology, Greene Pub. Associates and Wiley-Interscience (1988, including all updates until present), Ed Harlow and David Lane (editors) Antibodies: A Laboratory Manual, Cold Spring Harbour Laboratory, (1988), and J. E. Coligan et al., (editors) Current Protocols in Immunology, John Wiley & Sons (including all updates until present).

A polypeptide suitable for use in a method of the invention may be defined by the extent of identity (% identity) of its amino acid sequence to a reference amino acid sequence, or by having a greater % identity to one reference amino acid sequence than to another. The % identity of a polypeptide to a reference amino acid sequence is typically determined by GAP analysis (Needleman and Wunsch, 1970; GCG program) with parameters of a gap creation penalty=5, and a gap extension penalty=0.3. The query sequence is at least 100 amino acids in length and the GAP analysis aligns the two sequences over a region of at least 100 amino acids. Even more preferably, the query sequence is at least 250 amino acids in length and the GAP analysis aligns the two sequences over a region of at least 250 amino acids. Even more preferably, the query sequence is at least 450 amino acids in length and the GAP analysis aligns the two sequences over a region of at least 450 amino acids. Even more preferably, the GAP analysis aligns two sequences over their entire length.

The term “and/or”, e.g., “X and/or Y” shall be understood to mean either “X and Y” or “X or Y” and shall be taken to provide explicit support for both meanings or for either meaning.

Unless the context suggests otherwise, the mention of a term in singular such as sensor and substrate clearly means the plural as well. For instance, logically many individual sensor molecules will be flowed through the device or contained within a well rather than a single molecule.

As used herein, the term about, unless stated to the contrary, refers to +/−10%, more preferably +/−5%, even more preferably +/−1%, of the designated value.

Throughout this specification the word “comprise”, or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.

Unless indicated or the context indicates otherwise, % concentration is weight/volume (% w/v).

Sensor

Throughout the specification “sensor” and “sensor molecule” are used interchangeably.

In one aspect the present disclosure provides a sensor molecule for detecting a carbohydrate, the sensor comprising

i) a carbohydrate binding domain of a helix-turn-helix transcription factor, or a variant of the carbohydrate binding domain;

ii) a chemiluminescent donor domain; and

iii) an acceptor domain;

wherein the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain is altered when the carbohydrate binds to the carbohydrate binding domain.

In some embodiments, the sensor is a continuous stretch of amino acids (in other words, the sensor is a single polypeptide). For example, the carbohydrate binding domain, chemiluminescent donor protein domain and acceptor domain are a single stretch of amino acids such as, but not limited to, a chemiluminescent donor protein domain covalently attached to the N-terminus of the carbohydrate binding domain and an acceptor protein domain covalently attached to the C-terminus of the carbohydrate binding domain, or an acceptor protein domain covalently attached to the N-terminus of the carbohydrate binding domain and a chemiluminescent donor protein domain covalently attached to the C-terminus of the carbohydrate binding domain. Examples are provided in FIG. 1.

For example, in some embodiments, the polypeptide has a sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28 or a fragment or variant thereof. In some embodiments, the polypeptide can have a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28 or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof. As used herein, a “portion” of a polypeptide retains the relevant activity of the polypeptide, for example, the portion of the polypeptide retains the ability to bind the carbohydrate.

For example, in some embodiments, the polypeptide has a sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18 or a fragment or variant thereof. In some embodiments, the polypeptide can have a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof. In some embodiments, the polypeptide has a sequence selected from the group consisting of SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28 or a fragment or variant thereof. In some embodiments, the polypeptide can have a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof.

In some embodiments, there is also provided a nucleic acid which comprises a polynucleotide sequence encoding a sensor as defined herein. In some embodiments, the nucleic acid is an isolated nucleic acid. For example, in some embodiments, the nucleic acid molecule comprises a sequence encoding a polypeptide sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28. In some embodiments, the nucleic acid molecule comprises a sequence encoding a polypeptide sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18. In some embodiments, the nucleic acid molecule comprises a sequence encoding a polypeptide sequence selected from the group consisting of SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28. In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide sequence of SEQ ID NO: 15 or SEQ ID NO: 25. In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide sequence of SEQ ID NO: 15. In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide sequence of SEQ ID NO: 25. In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide having a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28 or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof. In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide having a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof. In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide having a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof. In some embodiments, the nucleic acid molecule comprises a sequence selected from the group consisting of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 and SEQ ID NO: 32, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof of any one of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 and SEQ ID NO: 32. In some embodiments, the nucleic acid molecule comprises a sequence selected from the group consisting of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21 and SEQ ID NO: 22, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof of any one of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21 and SEQ ID NO: 22. In some embodiments, the nucleic acid molecule comprises a sequence selected from the group consisting of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21 and SEQ ID NO: 22, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof of any one of SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 and SEQ ID NO: 32.

In another aspect, the present disclosure provides a sensor molecule for detecting lactose or lactulose comprising a bacterial BgaR transcription factor or variant thereof, covalently joined to a resonance energy transfer donor domain and a resonance energy transfer acceptor domain, wherein the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain is altered when lactose binds to the transcription factor. Binding of lactose or lactulose to the sensor molecules of this aspect produces a change in resonance energy transfer, for example a change in BRET or a change in FRET. In some embodiments, the present disclosure provides a sensor molecule for detecting lactose. In some embodiments, present disclosure provides a sensor molecule for detecting lactulose.

In some embodiments, the sensor is a continuous stretch of amino acids (in other words, the sensor is a single polypeptide). For example, the bacterial BgaR transcription factor or variant thereof, resonance energy transfer donor domain and resonance energy transfer acceptor domain are a single stretch of amino acids such as, but not limited to, a donor protein domain covalently attached to the N-terminus of the bacterial BgaR transcription factor and an acceptor protein domain covalently attached to the C-terminus of the bacterial BgaR transcription factor, or an acceptor protein domain covalently attached to the N-terminus of the bacterial BgaR transcription factor and a donor protein domain covalently attached to the C-terminus of the bacterial BgaR transcription factor.

For example, in some embodiments, the polypeptide has the sequence provided in SEQ ID NO: 23 or a fragment or variant thereof. In some embodiments, the polypeptide can have a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in SEQ ID NO: 23, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof.

In some embodiments, there is also provided a nucleic acid molecule which comprises a polynucleotide sequence encoding a sensor as defined herein. In some embodiments, the nucleic acid molecule is an isolated nucleic acid molecule. For example, in some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide sequence provided in SEQ ID NO: 23 or a fragment or variant thereof. In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide having a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence provided in SEQ ID NO: 23, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof. In some embodiments, the nucleic acid molecule comprises the sequence provided in SEQ ID NO: 24, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof.

The sensors, compositions, kits, methods and uses of the present disclosure encompass polypeptides and nucleic acids having the sequences specified, or sequences substantially identical or similar thereto, e.g., sequences at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence specified. In the context of an amino acid sequence, the term “substantially identical” is used herein to refer to a first amino acid that contains a sufficient or minimum number of amino acid residues that are i) identical to, or ii) conservative substitutions of aligned amino acid residues in a second amino acid sequence such that the first and second amino acid sequences can have a common structural domain and/or common functional activity. For example, amino acid sequences that contain a common structural domain having at least about 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to the sequence specified are termed substantially identical.

In the context of nucleotide sequence, the term “substantially identical” is used herein to refer to a first nucleic acid sequence that contains a sufficient or minimum number of nucleotides that are identical to aligned nucleotides in a second nucleic acid sequence such that the first and second nucleotide sequences encode a polypeptide having common functional activity, or encode a common structural polypeptide domain or a common functional polypeptide activity. For example, nucleotide sequences having at least about 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to the sequence specified are termed substantially identical.

Calculations of homology or sequence identity between sequences (the terms are used interchangeably herein) are performed using techniques know to the person skilled in the art. For example, to determine the percent identity of two amino acid sequences, or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). In a preferred embodiment, the length of a reference sequence aligned for comparison purposes is at least 30%, preferably at least 40%, more preferably at least 50%, 60%, and even more preferably at least 70%, 80%, 90%, 100% of the length of the reference sequence. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid “homology”).

The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.

The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. In some embodiments, the percent identity between two amino acid sequences is determined using the Needleman and Wunsch (1970) algorithm which has been incorporated into the GAP program in the GCG software package, using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. In yet other embodiments, the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package, using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6.

The percent identity between two amino acid or nucleotide sequences can be determined using the algorithm of Meyers and Miller (1989) which has been incorporated into the ALIGN program (version 2.0), using, for example, a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.

The nucleic acid and protein sequences described herein can be used as a “query sequence” to perform a search against public databases to, for example, identify other family members or related sequences. Such searches can be performed using, for example, the NBLAST and XBLAST programs (version 2.0) of Altschul, et al., (1990), as well as BLASTp. BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12 to obtain nucleotide sequences homologous to nucleic acid molecules of some embodiments of the invention. BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to protein molecules of some embodiments of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., (1997). When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., BLASTp, XBLAST and NBLAST) can be used. See http://www.ncbi.nlm.nih.gov/BLAST.

Nucleic acid molecules corresponding to natural allelic variants, homologs, orthologs, or other related sequences (e.g., paralogs) of the sequences described herein can be isolated based on their homology to the nucleic acids encoding the amino acid sequences disclosed herein, for example by performing standard or stringent hybridization reactions using all or a portion of the known sequences as probes. Such methods for nucleic acid hybridization and cloning are well known in the art.

The homologs of the peptides as provided herein typically have structural similarity with such peptides. A homolog of a polypeptide includes one or more conservative amino acid substitutions, which may be selected from the same or different members of the class to which the amino acid belongs.

In some embodiments, the sequences may also have deletions, insertions or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent substance. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues as long as the secondary binding activity of the substance is retained. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine, valine, glycine, alanine, asparagine, glutamine, serine, threonine, phenylalanine, and tyrosine.

Some embodiments of the present invention also encompass conservative substitution (substitution and replacement are both used herein to mean the interchange of an existing amino acid residue with an alternative residue) that may occur e.g., like-for-like substitution such as basic for basic, acidic for acidic, polar for polar, etc. Non-conservative substitution may also occur e.g., from one class of residue to another or alternatively involving the inclusion of unnatural amino acids such as ornithine (hereinafter referred to as Z), diaminobutyric acid ornithine (hereinafter referred to as B), norleucine ornithine (hereinafter referred to as O), pyridylalanine, thienylalanine, naphthylalanine and phenylglycine. Conservative substitutions that may be made are, for example, within the groups of basic amino acids (arginine, lysine and histidine), acidic amino acids (glutamic acid and aspartic acid), aliphatic amino acids (alanine, valine, leucine, isoleucine), polar amino acids (glutamine, asparagine, serine, threonine), aromatic amino acids (phenylalanine, tryptophan and tyrosine), hydroxyl amino acids (serine, threonine), large amino acids (phenylalanine and tryptophan) and small amino acids (glycine, alanine).

In addition to the sequence encoding the sensor molecule of the invention, the nucleic acid molecule may contain other sequences such as primer sites, transcription factor binding sites, vector insertion sites and sequences which resist nucleolytic degradation (e.g. polyadenosine tails). The nucleic acid molecule may be DNA or RNA and may include synthetic nucleotides, provided that the polynucleotide is still capable of being translated in order to synthesize a protein of the invention.

In some embodiments, the nucleic acid forms part of a vector such as a plasmid. In addition to the nucleic acid sequence described above, the plasmid comprises other elements such as a prokaryotic origin of replication (for example, the E. coli OR1 origin of replication) an autonomous replication sequence, a centromere sequence; a promoter sequence capable of expressing the nucleic acid in the host cell which is operably linker to the nucleic acid, a terminator sequence located downstream of the nucleic acid sequence, an antibiotic resistance gene and/or a secretion signal sequence. A vector comprising an autonomous replication sequence is also a yeast artificial chromosome. In some alternative embodiments, the vector is a virus, such as a bacteriophage and comprises, in addition to the nucleic acid sequence of the invention, nucleic acid sequences for replication of the bacteriophage, such as structural proteins, promoters, transcription activators and the like.

The nucleic acid or vector of the invention may be used to transfect or transform host cells in order to synthesize the sensor molecule of the present disclosure. Suitable host cells include prokaryotic cells such as E. coli and eukaryotic cells such as yeast cells, or mammalian or plant cell lines. Host cells are transfected or transformed using techniques known in the art such as electroporation; calcium phosphate base methods; a biolistic technique or by use of a viral vector.

After transfection/transformation, the nucleic acid or vector of the invention is transcribed as necessary and translated. In some embodiments, the synthesized protein is extracted from the host cell, either by virtue of its being secreted from the cell due to, for example, the presence of secretion signal in the vector, or by lysis of the host cell and purification of the protein therefrom. In some embodiments, there is provided a process for producing a sensor molecule as defined herein, the process comprising cultivating a host cell or a vector as defined herein under conditions which allow expression of the polynucleotide encoding the polypeptide, and recovering the expressed polypeptide.

In some embodiments, the sensor is provided as a cell-free composition. As used herein, the term “cell free composition” refers to an isolated composition which contains few, if any, intact cells and which comprises the sensor. Examples of cell free compositions include cell (such as yeast cell) extracts and compositions containing an isolated and/or recombinant sensor molecules (such as proteins). Methods for preparing cell-free compositions from cells are well-known in the art.

The sensor molecules optionally comprise at least one linker. For example, the sensor may comprise a linker which connects the carbohydrate binding domain (or helix-turn-helix transcription factor comprising the carbohydrate binding domain) to the chemiluminescent donor domain and/or acceptor domain. In another example, the sensor molecule may comprise a linker at the N- and/or C-terminus of the sensor molecule. In some embodiments, the sensor molecule comprises at least one peptide linker. In some embodiments, a linker can be located at the N- and/or C-terminus of the carbohydrate binding domain (or helix-turn-helix transcription factor comprising the carbohydrate binding domain). Preferably the linker is a peptide or polypeptide. In some embodiments, the linker comprises one or more glycine, serine and/or threonine residues. For example, in some embodiments, the linker comprises an amino acid sequence selected from GSSGGS (SEQ ID NO: 2), GGSGGS (SEQ ID NO: 3), GGTGGG (SEQ ID NO: 4), GGGGGT (SEQ ID NO: 5) LQGGTGGG (SEQ ID NO: 6), FEGGTGGG (SEQ ID NO: 7) and GGSGGSL (SEQ ID NO: 8). In some embodiments, the linker is 25 amino acids or less, 20 amino acids or less, 15 amino acids or less, 10 amino acids or less, 8 amino acids or less, 6 amino acids or less, 4 amino acids or less, or 3 amino acids or less. In some embodiments, the linker is between 1 and 10 amino acids in length, between 2 and 9 amino acids in length or between 4 and 8 amino acids in length. The linker sequence can be located at the N-terminus of the carbohydrate binding domain, the C-terminus of the carbohydrate binding domain or both. When a linker is located at both the N- and C-terminus, the linker sequence can be the same or different. Without wishing to be bound by theory, the linker may serve one or more of the following purposes: (i) help ensure that the carbohydrate binding site is in a preferred conformation for binding; (ii) improve the accessibility of the carbohydrate binding site; (iii) increase the magnitude of the change in spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain (for example, the linker sequence can function to increase the BRET ratio); and/or (iv) optimise the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain.

In some embodiments, the sensor further comprises protease cleavage sites and/or purification tags. In some embodiments, the linker comprises an amino acid or series of amino acids than can be used for purification and/or for attachment of the chemiluminescent donor domain and/or acceptor domain. For example, the linker can comprise a histidine tag for purification or self-assembly with the chemiluminescent donor domain and/or acceptor domain. In another example, the linker can comprise a reactive group (e.g. cysteine or lysine) for addition of the chemiluminescent donor domain and/or acceptor domain. In some embodiments, the sensor comprises a protease cleavage site. The protease cleavage site may be used to remove purification tags.

The polypeptides of the invention can be produced in a variety of ways, including production and recovery of natural polypeptides, production and recovery of recombinant polypeptides, and chemical synthesis of the polypeptides. In one embodiment, an isolated polypeptide is produced by culturing a cell capable of expressing the polypeptide under conditions effective to produce the polypeptide, and recovering the polypeptide. Effective culture conditions can be determined by the person skilled in the art include, but are not limited to, effective media, bioreactor, temperature, pH and oxygen conditions that permit polypeptide production. An effective medium refers to any medium in which a cell is cultured to produce a polypeptide. Such medium typically comprises an aqueous medium having assimilable carbon, nitrogen and phosphate sources, and appropriate salts, minerals, metals and other nutrients, such as vitamins. Cells can be cultured in conventional fermentation bioreactors, shake flasks, test tubes, microtiter dishes, and petri plates. Culturing can be carried out at a temperature, pH and oxygen content appropriate for a recombinant cell. Such culturing conditions are within the expertise of one of ordinary skill in the art.

The polypeptides of the present invention may be extracted and purified from recombinant cells, such as plant, bacteria or yeast cells, producing said polypeptide by methods known to the person skilled in the art. In one embodiment, the method involves extracting total soluble proteins by homogenizing cells/tissues/plants and isolating the hexa-histidine polypeptide using a Ni-NTA or Talon. Additional purification may be achieved with conventional gel or affinity chromatography.

Carbohydrate

The sensors of the present disclosure are capable of binding to carbohydrates. The term “carbohydrate” as used herein is defined broadly and refers to monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides, for example by reduction of the carbonyl group (forming alditols), by oxidation of one or more terminal groups to carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom, an amino group, thiol group or similar groups (forming a derivative). It also includes derivatives of these compounds (see IUPAC. Compendium of Chemical Terminology, 2nd ed. (the “Gold Book”) compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997)). As the person skilled in the art would be aware, carbohydrates can contain asymmetric centers and therefore have stereoisomers. The carbohydrates useful in the sensors, methods, kits and compositions of this disclosure may be in either the D-stereoisomeric and/or the L-forms (enantiomers) form. Both the open chain and closed ring structure fall within the definition of carbohydrate.

In some embodiments, the carbohydrate is a sugar or a sugar derivative.

In some embodiments, the carbohydrate is a sugar. As used herein, the term “sugar” includes both polyhydroxyaldehydes and polyhydroxyketones comprising at least one hydroxyl group and at least one aldehyde group or ketone group. In some embodiments, the sugar is a monosaccharide, oligosaccharide or polysaccharide. Suitable monosaccharides can include trioses (such as glyceraldehyde), tetroses (such as erythrose and threose), pentoses (such as ribulose, arabinose, xylose, ribose and lyxose), hexoses (such as glucose, mannose, galactose, idose, gulose, fructose, altrose, allose, fucose and talose), heptoses (such as sedoheptulose), octoses (such as glycero-D-manno-octulose) and pentose ring sugars (such as ribofuranose and ribopyranose). In some embodiments, the monosaccharide is selected from the group consisting of ribose, glucose, mannose, galactose, and fructose. As used herein, an “oligosaccharide” is a saccharide polymer containing between two to ten saccharides which are linked by a glycosidic bond. In some embodiments, the oligosaccharide comprises two, three, four, five, six, seven, eight, nine or ten saccharides. For example, oligosaccharides include, but are not limited to, disaccharides or trisaccharides. Suitable oligosaccharides include, but are not limited to, sucrose, lactose, lactulose, trehalose, gentiobiose, maltose, isomaltose, cellobiose melezitose, raffinose, stachyose, cellotriose, melibiose and verbascose. Suitable oligosaccharides include, but are not limited to, sucrose, lactose, trehalose, gentiobiose, maltose, isomaltose, cellobiose melezitose, raffinose, stachyose, cellotriose, melibiose and verbascose. In some embodiments, the carbohydrate is a disaccharide. In some embodiments, the carbohydrate is lactose or lactulose. In some embodiments, the carbohydrate is lactose. In some embodiements, the carbohydrate is lactulose. In preferred embodiments, the carbohydrate is lactose. Polysaccharides are sugars in which monosaccharides or oligosaccharides are chemically linked together via glycosidic bonds. Suitable polysaccharides include, but are not limited to, amylose, amylopectin and glycogen.

In some embodiments, the carbohydrate is a sugar derivative. As used herein, a “sugar derivative” refers to a sugar which has been modified to replace one or more hydroxy groups with a different substituent, or a sugar variant obtained by an oxidation-reduction reaction of a sugar. Suitable substituents include, but is not limited to, alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkenyl, substituted alkenyl, cycloalkenyl, substituted cycloalkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, carbocyclic group, substituted carbocyclic group, heterocyclic group, substituted heterocyclic group, halogen, hydroxy, substituted hydroxy, thiol, substituted thiol, cyano, phospho, substituted phospho, nitro, amino, substituted amino, carboxy, substituted carboxy, acyl, substituted acyl, thiocarboxy, substituted thiocarboxy, amide, substituted amide, substituted carbonyl, substituted thiocarbonyl, substituted sulfonyl and substituted sulfinyl. In some embodiments, the sugar derivative is selected from the group consisting of a sugar alcohol (also referred to as an alditol or aldose alcohol), ketose, amino sugar (or glycosylamine), deoxy sugar, sugar phosphate, acidic sugar, glycoside, and lactone. Suitable sugar alcohols include, but are not limited to, erythritol, glucitol, sorbitol, or mannitol. Suitable ketoses include, but are not limited to, dihydroxyacetone, erythrulose, ribulose, xylulose, psicose, fructose, sorbose, and tagatose. Suitable amino sugars include, but are not limited to, glucosamine, galactosamine, N-acetylglucosamine, N-acetylgalactosamine, muramic acid, N-acetyl muramic acid, and N-acetylneuraminic acid (sialic acid). Suitable glycosides include, but are not limited to, glucopyranose and methyl-glucopyranose. Suitable lactones include, but are not limited to, gluconolactone. Suitable deoxy sugars, include but are not limited to, deoxyribose and rhamnose. Suitable sugar phosphates include, but are not limited to, glucose 6-phosphate, fructose 6-phosphate, erythrose 4 phosphate, ribose 5-phosphate, fructose-1,6-bisphosphate and xylulose 5-phosphate.

In some embodiments, the carbohydrate is a substance derived from a monosaccharide. In some embodiments, the carbohydrate is a substance derived from a monosaccharide by reduction of the carbonyl group or by oxidation of one or more terminal groups to carboxylic acids. For example the substance derived from a monosaccharide can be, but is not limited to, alditols (such as erythritol, glucitol, sorbitol, or mannitol) and sugar acids (such as gluconic acid, mannonic acid, threonic acid and glyceric acid). In some embodiments, the substance derived from a monosaccharide is selected from the group consisting of lactate and pyruvate.

Carbohydrate Binding Domains

As used herein, a “carbohydrate binding domain” is a polypeptide capable of binding to a carbohydrate. Carbohydrate binding domains comprise at least one binding site that binds to a carbohydrate. The term “binding to a carbohydrate” refers to non-covalent binding of a carbohydrate to a carbohydrate binding domain. Such binding may involve non-covalent interactions such as salt bridges, hydrogen bonds, van der Waal forces, stacking forces, complex formation or combinations thereof between the carbohydrate and the carbohydrate binding domain binding domain. It may also include interactions with water molecules in the binding site.

Suitable carbohydrate binding domains may be present on a polypeptide chain that consists solely of the binding domain amino acid sequence or may be present in the context of a larger polypeptide molecule (i.e., one which comprises amino acids other than those of the binding domain). Accordingly, the carbohydrate binding domain may be a full-length protein (for example, a full length helix-turn-helix transcription factor) or a fragment (for example, a fragment of a helix-turn-helix transcription factor comprising a carbohydrate binding domain) or variant thereof. The carbohydrate binding domain can comprise either natural or non-natural amino acid sequences. The minimum length of the carbohydrate binding domain which maintains binding to the carbohydrate and undergoes a conformational change which is sufficient and suitable for carbohydrate detection as described herein can be determined by the person skilled in the art.

In some embodiments, the carbohydrate binding domain is a naturally occurring polypeptide. In some embodiments, the carbohydrate binding domain is a variant of a naturally occurring polypeptide. For example, in some embodiments, the carbohydrate binding domain is an amino acid that is altered (i.e., by insertion, deletion or substitution of at least one amino acid or nucleotide, as the case may be) such that the carbohydrate binding domain sequence is no longer as found in nature. In some embodiments, the position of the variation is within the residues which form the carbohydrate binding domain. The variant may comprise either natural or non-natural amino acid sequences. In some embodiments, the variant carbohydrate binding domain comprises an amino acid sequence which at least 30% identical to a naturally occurring carbohydrate binding domain of a helix-turn-helix transcription factor. For example, in some embodiments, the variant carbohydrate binding domain comprises an amino acid sequence which is at least 30% identical, at least 35% identical, at least 40% identical, at least 45% identical, at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, or at least 99.5% identical to a naturally occurring carbohydrate binding domain of a helix-turn-helix transcription factor.

In some embodiments, the carbohydrate binding domain is a sugar or sugar derivative binding domain. In some embodiments, the carbohydrate binding domain is a sugar binding domain. In some embodiments, the carbohydrate binding domain is a sugar derivative binding domain.

In some embodiments, the carbohydrate binding domain binds to a carbohydrate with a high affinity. In some embodiments, the carbohydrate binding domain binds to a carbohydrate with half-maximal binding occurring at a carbohydrate concentration of 1 nM or below, 10 nM or below, 50 nM or below, 100 nM or below, 500 nM or below, 1 μM or below, 10 μM or below, 50 μM or below, 100 μM or below, 500 μM or below, 1 mM or below or 10 mM or below. For example, in some embodiments the EC₅₀ is between approximately 0.1 μM and 150 μM, between approximately 1 μM and 100 μM or between approximately 5 μM and 50 μM. In some embodiments, the EC₅₀ is between approximately 10 μM and 25 μM. Alternatively, in some embodiments the EC₅₀ is between approximately 0.1 mM and 150 mM, between approximately 1 mM and 100 mM, between approximately 2 mM and 50 mM or between approximately 2 mM and 5 mM.

Upon binding of a carbohydrate to the carbohydrate binding domain, a suitable carbohydrate binding domains undergo a conformational change which is sufficient and suitable for carbohydrate detection as described herein.

Carbohydrate binding domains useful in the sensors of the present disclosure are derived from transcription factors which contain a helix-turn-helix (HTH) domain (also referred to as a helix-turn-helix motif). That is, the sensors comprise a carbohydrate binding domain of a helix-turn-helix transcription factor, or a variant of the carbohydrate domain. In some embodiments, the sensor molecule comprises the carbohydrate binding domain of a helix-turn-helix transcription factor and one or more additional amino acids present in the helix-turn-helix transcription factor. For example, the sensor may also comprise one or more functional domains (for example, the DNA binding domain) also present in the helix-turn-helix transcription factor. In one embodiment, the polypeptide lacks the helix-turn-helix domain of the transcription factor. In an alternate embodiment, the polypeptide has the helix-turn-helix domain of the transcription factor. Any variant, portion or fragment useful in the sensors described herein retains the ability to bind to a carbohydrate. In some embodiments, the carbohydrate binding domain comprises a protein fold disclosed to bind to a carbohydrate. Non-limiting examples of protein folds which bind to a carbohydrate include the Nudix hydrolase fold, a carbohydrate-binding module, or the AraC carbohydrate recognition domain.

In some embodiments, the HTH transcription factor is a bacterial HTH transcription factor. In some embodiments, the HTH transcription factor may originate from gram-negative bacteria or gram-positive bacteria. Examples of such HTH transcription factors are shown in Table 1. Naturally occurring species variants of the HTH transcription factors listed in Table 1 can also be used, in addition to variants or fragments thereof as discussed herein. Homologues (such as orthologues originating from related species of bacteria) of the HTH transcription factors listed in Table 1 can also be used in the sensor molecules described herein. Moreover, it is contemplated that the term “HTH transcription factor” includes variants, portion, fragments or derivatives of any naturally occurring HTH transcription factor as long as the variant, portion, fragment or derivative retains the ability to bind a carbohydrate. It is also to be understood that the person skilled in the art is capable of modifying and optimizing naturally occurring HTH transcription factors by suitable techniques known in the art such as in vitro or in vivo mutagenesis, PCR shuffling mutagenesis, chemical modification and the like.

TABLE 1 Exemplary helix-turn-helix transcription factors Example Accession Transcription number (from Factor Sugar or sugar derivative UniProt) YvoA/NgaR N-acetylglucosamine O34817, Q795E9, (GlcNAc)/glucosamine-6- phosphate TrmB maltose, trehalose, maltotriose, Q7LYW4, Q9HGZ9, longer maltodextrins, sucrose, Q9HPW0 and glucose AraR arabinose A2QJX5, Q5BGE2, P96711 AraC arabinose P0A9E0, P96711 TreR trehalose-6-phosphate P36673, P39796, P36674 MurQ N-acetylmuramic acid P76535, Q45582, (MurNAc)-6-phosphate Q8ZN25 LacI allolactose P03023, BgaR lactose Q8XMB9, BAB80476, Q6PU53, O52846, A0A069CWF6, H1X564, Q6PU52 EbgR lactose P06846 CebR cellobiose, cellotriose D2Q7B0, A0A173WKF3 CggR fructose-1,6- O32253 biphosphate FruR D-fructose P0ACP1, O31713 GalR D-galactose E1WAQ4, Q9ZB11 GalS galactose, D-fucose P25748, P41030 MalI maltose P18811, P96158 MelR melibiose P0ACH8, P0ACH9 RafR raffinose P21867, P43465 RbtR D-ribulose P07760 XylR D-xylose P06519 ScrR D-fructose P37077, P37076 MsmR melibiose O34829, Q00753 XylS D-xylose P07859

In some embodiments, the HTH transcription factor is a member of the G_(NT)R family of transcription factors. The G_(NT)R family, named after the gluconate operon repressor in Bacillus subtilis, is one of the most prevalent superfamilies of HTH transcription factors (Haydon and Guest, 1991; Zheng et al., 2009). This family of HTH proteins generally has DNA-binding domain and an effector binding domain (Aravind and Anantharaman, 2003; Rigali et al., 2002; Rigali et al., 2004). The DNA-binding domain is relatively conserved amongst members of this superfamily with a central 0-sheet cluster and three α-helices, two of which, along with a connective loop, constitute the HTH motif (Zheng et al., 2009; Rigali et al., 2002; Kong et al., 2009). In contrast, the effector domain is diverse amongst the G_(NT)R superfamily and their structural divergence leads to six subfamilies of G_(NT)R transcriptional factors: four main subfamilies (FadR, HutC, MocR, YtrA) and two minor subfamilies (AraR and PlmA) (Zheng et al., 2009; Rigali et al., 2002; Rigali et al., 2004; Wiethaus et al., 2008; Lee et al., 2003; Zhang et al., 2012; Franco et al., 2006; Franco et al., 2007). The effector domain typically binds to molecules, for example carbohydrates. Typically, G_(NT)R family members have an N-terminal DNA binding domain and a C-terminal effector binding. However, in the AraR subfamily the DNA-binding domain is typically located at the C-terminal end whereas the effector binding-domain is found at the N-terminal end.

One example of a suitable bacterial HTH transcription factor is BgaR. BgaR is a transcription factor from Clostridium perfringins strain 13 (CPE0770; UniProt Accession Number: Q8XMB9) and is a putative member of the AraR subfamily (Hartman et al., 2011). BgaR binds to lactose and forms part of a lactose-inducible regulatory system.

In some embodiments, the sensor comprises the helix-turn-helix transcription factor BgaR or a fragment or variant thereof. In some embodiments, the carbohydrate binding domain comprises an amino acid sequence provided as SEQ ID NO: 1 or is a fragment or variant thereof. In some embodiments, the carbohydrate binding domain has an amino acid sequence which is at least 30% identical, at least 35% identical, at least 40% identical, at least 45% identical, at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, at least 99.5% identical to that provided in SEQ ID NO: 1. In some embodiments, the carbohydrate binding domain has an amino acid sequence which is at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof (e.g., a portion comprising amino acids 1-179, amino acids 1-171, 1-157, amino acids 1-150, amino acids 12-179, amino acids 12-171, amino acids 12-150, amino acids 16-179, amino acids 16-171, amino acids 16-151 or amino acids 16-129 of SEQ ID NO: 1). In some embodiments, the carbohydrate binding domain comprises an amino acid sequence provided as SEQ ID NO: 9 or is a fragment or variant thereof that retains carbohydrate binding activity. In some embodiments, the carbohydrate binding domain has an amino acid sequence which is at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 9.

The minimum carbohydrate binding domain of BgaR (or another HTH transcription factor) can be determined using techniques known to the person skilled in the art. For example, the protein sequence described herein can be used as a “query sequence” to perform a search against the conserved domain database to, for example, identify the putative carbohydrate binding domain and/or HTH domain (Marchler-Bauer et al., 2017; Marchler-Bauer et al., 2015; Marchler-Bauer et al., 2011; Marchler-Bauer and Bryant, 2004). When searching for conserved domains using the conserved domain database, the default parameters can be used. See https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. The ability of the predicted carbohydrate binding domain to bind carbohydrates can be confirmed using techniques known to the person skilled in the art.

In some embodiments, the carbohydrate binding domain of BgaR comprises amino acids 1-179, amino acids 1-171, amino acids 1-157, amino acids 1-150, amino amino acids 12-179, amino acids 12-171, amino acids 12-157, amino acids 12-150, amino acids 16-179, amino acids 16-171, amino acids 16-157, acids 16-151 or amino acids 16-129 of SEQ ID NO: 1. In some embodiments, the carbohydrate binding domain of BgaR comprises amino acids 1-150, amino acids 1-171, amino acids 1-179, amino acids 12-171 or amino acids 12-150 of SEQ ID NO: 1. In some embodiments, the carbohydrate binding domain has an amino acid sequence which is at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to amino acids 1-157, amino acids 16-151 or amino acids 16-129 of SEQ ID NO: 1. In some embodiments, the carbohydrate binding domain has an amino acid sequence which is at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to amino acids 1-150, amino acids 1-171, amino acids 12-150 or amino acids 12-171 of SEQ ID NO: 1. In some embodiments, the carbohydrate binding domain comprises an amino acid sequence provided as SEQ ID NO: 9. In some embodiments, the carbohydrate binding domain has an amino acid sequence which is at least 30% identical, at least 35% identical, at least 40% identical, at least 45% identical, at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, at least 99.5% identical, or 100% identical to that provided in SEQ ID NO: 9. In some embodiments, the carbohydrate binding domain has an amino acid sequence which is at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion of SEQ ID NO: 9 or at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion of SEQ ID NO: 9.

Other suitable transcription factors can be identified by the person skilled in the art using tools such as BLASTp. For example, in some embodiments the transcription factor comprises a carbohydrate binding domain that comprises an amino acid sequence which is at least 30% identical, at least 35% identical, at least 40% identical, at least 45% identical, at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, at least 99.5% identical to the carbohydrate binding domain of BgaR (for example, the amino acids in SEQ ID NO: 9 or to amino acids 1-179, amino acids 1-171, amino acids 1-150, amino acids 12-179, amino acids 12-171 or amino acids 12-150). Suitable transcription factors include, but are not limited to, putative lactose operon transcription activator from Clostridium perfringens (UniProt Accession No: A0A133MUX6), AraC family transcriptional regulator (Clostridium perfringens D str. JGS1721) (UniProt Accession No: B1V7NO), AraC family transcriptional regulator (Clostridium perfringens) (UniProt Accession No: A0A127EGD8), arabinose operon regulatory protein (uncultured Clostridium sp.) (UniProt Accession No: A0A1C6JUB7), transcriptional regulator (Clostridium disporicum) (UniProt Accession No: A0A174HYB7), arabinose operon regulatory protein (uncultured Clostridium sp.) (UniProt Accession No: A0A1C6KY47), transcriptional regulator (Clostridium disporicum) (UniProt Accession No: A0A174LZQ7), AraC family transcriptional regulator (Clostridium paraputrificum) (UniProt Accession No: A0A1741591), uncharacterized protein (Clostridium butyricum 60E.3) (UniProt Accession No: N9YR91), AraC family transcriptional regulator (Clostridium neonatale) (UniProt Accession No: A0A2A7ME67), AraC family transcriptional regulator (Staphylococcus intermedius NCTC 11048) (UniProt Accession No: A0A2K4AZL9). AraC family transcriptional regulator (Staphylococcus pseudintermedius) (UniProt Accession No: A0A166PPM9), AraC family transcriptional regulator (Staphylococcus hyicus) (UniProt Accession No: A0A2T4R7G1), AraC family transcriptional regulator (Staphylococcus delphini) (UniProt Accession No: A0A2A4HCU9), AraC family transcriptional regulator (Staphylococcus agnetis) (UniProt Accession No: A0A2T4MS83), Lactose operon transcription activator (Staphylococcus xylosus) (UniProt Accession No: 033813), Lactose operon transcription activator (Staphylococcus saprophyticus) (UniProt Accession No: A0A1D4LKB2), Putative lactose operon transcription activator (Staphylococcus sinulans) (UniProt Accession No: A0A133QVV5), Transcriptional regulator, AraC family (Lactococcus lactis subsp. lactis strain KF147) (UniProt Accession No: A9QSR3.

In some embodiments, the sensor comprises a transcription factor comprising an amino acid sequence selected from the group consisting of the amino acid sequence provided in SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54 and SEQ ID NO: 55, or is a fragment or variant thereof. In some embodiments, the sensor comprises a transcription factor having an amino acid sequence which is at least 30% identical, at least 35% identical, at least 40% identical, at least 45% identical, at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, at least 99.5% identical to that provided in SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54 or SEQ ID NO: 55, or is a fragment or variant thereof.

In some embodiments, the carbohydrate binding domain comprises an amino acid sequence selected from the group consisting of the amino acid sequence provided in SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73 or SEQ ID NO: 74, or is a fragment or variant thereof. In some embodiments, the carbohydrate binding domain has an amino acid sequence which is at least 30% identical, at least 35% identical, at least 40% identical, at least 45% identical, at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, at least 99.5% identical to the amino acid sequence provided in SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73 or SEQ ID NO: 74, or is a fragment or variant thereof.

In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide having a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 or SEQ ID NO: 28, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof (e.g., a portion comprising amino acids 11-349, amino acids 18-349, amino acids 28-349, amino acids 38-349, or amino acids 39-349 of any one of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 or SEQ ID NO: 28). In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide having a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 or SEQ ID NO: 18, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof (e.g., a portion comprising amino acids 11-349, amino acids 18-349, amino acids 28-349, amino acids 38-349, or amino acids 39-349 of any one of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 or SEQ ID NO: 18). In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide having a sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 or SEQ ID NO: 28, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof (e.g., a portion comprising amino acids 11-349, amino acids 18-349, amino acids 28-349, amino acids 38-349, or amino acids 39-349 of any one of SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 or SEQ ID NO: 28).

In some embodiments, the nucleic acid molecule comprises a sequence selected from the group consisting of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21 and SEQ ID NO: 22 or a fragment or variant thereof. In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide having a sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21 and SEQ ID NO: 22, or a sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof of any one of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21 and SEQ ID NO: 22. In some embodiments, the nucleic acid molecule comprises a sequence selected from the group consisting of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 and SEQ ID NO: 32 or a fragment or variant thereof. In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide having a sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21 and SEQ ID NO: 22, or a sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof of any one of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 and SEQ ID NO: 32. In some embodiments, the nucleic acid molecule comprises a sequence selected from the group consisting of SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 and SEQ ID NO: 32 or a fragment or variant thereof. In some embodiments, the nucleic acid molecule comprises a sequence encoding the polypeptide having a sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence shown in any one of SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21 and SEQ ID NO: 22, or a sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof of any one of SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 and SEQ ID NO: 32.

The sensors, compositions, methods and uses of the present disclosure encompass polypeptides and nucleic acids having the sequences specified, or sequences substantially identical or similar thereto, e.g., sequences at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical or higher to the sequence specified. In the context of an amino acid sequence, the term “substantially identical” is used herein to refer to a first amino acid that contains a sufficient or minimum number of amino acid residues that are i) identical to, or ii) conservative substitutions of aligned amino acid residues in a second amino acid sequence such that the first and second amino acid sequences can have a common structural domain and/or common functional activity. For example, amino acid sequences that contain a common structural domain having at least about 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or 100% identity to the sequence specified are termed substantially identical.

Resonance Energy Transfer

Binding of a carbohydrate, such as lactose, to the sensors of the present disclosure can result in a change in Resonance Energy Transfer (RET), including, but not limited to, bioluminescent resonance energy transfer (“BRET”) and fluorescence resonance energy transfer (“FRET”).

As used herein, “BRET” is a proximity assay based on the non-radiative transfer of energy between a bioluminescent protein donor and an acceptor molecule. “Bioluminescent resonance energy transfer” and “BRET” are used interchangeably.

As used herein, “FRET” is a proximity assay based on the non-radiative transfer of energy between two chromophores, for example, two fluorophores. “FRET” and “fluorescence resonance energy transfer” are used interchangeably.

In one aspect, the sensor molecule comprises a donor domain and an acceptor domain covalently attached to the transcription factor or fragment or variant thereof. In some embodiments, the donor domain is a chemiluminescent donor domain. In alternative embodiments, the donor domain is a fluorophore. In some embodiments, the acceptor domain is a fluorescent acceptor domain, such as a fluorophore.

In some embodiments, the donor domain is covalently attached to the N-terminus of the transcription factor or fragment or variant thereof and the acceptor domain is covalently attached to the C-terminus of the transcription factor or fragment or variant thereof. In alternative embodiments, the donor domain is covalently attached to the C-terminus of the transcription factor or fragment or variant thereof and the acceptor domain is covalently attached to the N-terminus of the transcription factor or fragment or variant thereof.

A. Donor Domain

The sensor molecules of the present disclosure comprise a donor domain. The donor domain is capable of serving as a donor domain in a resonance energy transfer pair (for example, in a BRET pair or a FRET pair) and, depending on context, is also referred to herein as a “resonance energy transfer donor domain”. As used herein, the term “donor” means a molecule that emits light, for example a molecule which, when irradiated with light of a certain wavelength, emits light or a molecule which causes the emission of light as the result of a chemical reaction. Suitable donor domains include chemiluminescent domains and fluorescent domains.

In some preferred embodiments, the donor domain capable of serving as a donor domain in a BRET pair. For example, the donor domain can be a chemiluminescent donor domain. Chemiluminescence is the emission of energy with limited emission of heat (luminescence), as the result of a chemical reaction. The term “chemiluminescence” is used herein to encompass bioluminescence, which relies upon the activity of an enzyme. Non-enzymatic chemiluminescence is the result of chemical reactions between an organic dye and an oxidizing agent in the presence of a catalyst. Chemiluminescence emission occurs as the energy from the excited states of organic dyes, which are chemically induced, decays to ground state. The duration and the intensity of the chemiluminescence emission are mostly dependent on the extent of the chemical reagents present in the reaction solution.

In preferred embodiments, the chemiluminescent donor domain is a bioluminescent protein. As used herein, the term “bioluminescent protein” refers to any protein capable of acting on a suitable substrate to generate luminescence.

It is understood in the art that a bioluminescent protein is an enzyme which converts a substrate into an activated product which then releases energy as it relaxes. The activated product (generated by the activity of the bioluminescent protein on the substrate) is the source of the bioluminescent protein-generated luminescence that is transferred to the acceptor molecule.

There are a number of different bioluminescent proteins that can be employed in this invention (see, for example, Table 2). Light-emitting systems have been known and isolated from many luminescent organisms including bacteria, protozoa, coelenterates, molluscs, fish, millipedes, flies, fungi, worms, crustaceans, and beetles, particularly click beetles of genus Pyrophorus and the fire flies of the genera Photinus, Photuris, and Luciola. Additional organisms displaying bioluminescence are listed in WO 00/024878, WO 99/049019 and Viviani (2002).

TABLE 2 Exemplary bioluminescent proteins. MW Emission Example of Species Name Organism kDa × 10⁻³ (nm) Substrate Insect FFluc Photinus pyralis ~61 560 D-(−)-2-(6′- (North American hydroxybenzothiazolyl)- Firefly) D²-thiazoline-4- carboxylic acid, HBTTCA (C₁₁H₈N₂O₃S₂) (luciferin) Insect FF′luc Luciola cruciata 560-590 Luciferin (Japanese Firefly) (many mutants) Insect Phengodid beetles (railroad worms) Insect Arachnocampa spp. Luciferin Insect Orphelia fultoni (North American glow worm) Insect Clluc Pyrophorus plagiophthalamus 546, 560, Luciferin (click beetle) 578 and 593 Jellyfish Aequorin Aequorea 44.9 460-470 Coelenterazine Sea pansy RLuc Renilla reniformis 36 480 Coelenterazine Sea pansy RLuc8 Renilla reniformis 36 487 (peak) Coelenterazine/ (modified) (modified) Deep Blue C Sea pansy RLuc2 Renilla reniformis 36 480 Coelenterazine (modified) (modified) M185V/Q235A) Sea pansy RLuc Renilla reniformis 36 535 Coelenterazine (modified) 8.6-535 (modified) Sea pansy Rmluc Renilla mullerei 36.1 ~480 Coelenterazine Sea pansy Renilla kollikeri Crustacea Vluc Vargula hilgendorfii ~62 ~460 Coelenterazine (shrimp) Crustaeca CLuc Cypridina 75 465 Coelenterazine/ (sea firefly) Cypridina luciferin Dinofagellate Gonyaulax polyedra 130 ~475 Tetrapyrrole (marine alga) Mollusc Latia 170 500 Enol formate, (fresh water limpet) terpene, aldehyde Hydroid Obelia biscuspidata ~20 ~470 Coelenterazine Shrimp Oplophorus gracilorostris 31 462 Coelenterazine Shrimp Oplophorus gracilorostris 19 ~460 Furimazine (NanoLuc) Others Ptluc Ptilosarcus ~490 Coelenterazine Gluc Gaussia ~20 ~475 Coelenterazine Plluc Pleuromamma 22.6 ~475 Coelenterazine

Any suitable bioluminescent protein can be used in the sensors of the present disclosure. One very well-known example is the class of proteins known as luciferases which catalyse an energy-yielding chemical reaction in which a specific biochemical substance, a luciferin (a naturally occurring fluorophore), is oxidized by an enzyme having a luciferase activity (Hastings, 1996). A great diversity of organisms, both prokaryotic and eukaryotic, including species of bacteria, algae, fungi, insects, fish and other marine forms can emit light energy in this manner and each has specific luciferase activities and luciferins which are chemically distinct from those of other organisms. Luciferin/luciferase systems are very diverse in form, chemistry and function. Bioluminescent proteins with luciferase activity are thus available from a variety of sources or by a variety of means. Examples of bioluminescent proteins with luciferase activity may be found in U.S. Pat. Nos. 5,229,285, 5,219,737, 5,843,746, 5,196,524, and 5,670,356. Two of the most widely used luciferases are: (i) Renilla luciferase (from R. reniformis), a 35 kDa protein, which uses coelenterazine as a substrate and emits light at 480 nm (Lorenz et al., 1991); and (ii) Firefly luciferase (from Photinus pyralis), a 61 kDa protein, which uses luciferin as a substrate and emits light at 560 nm (de Wet et al., 1987).

Gaussia luciferase (from Gaussia princeps) has been used in biochemical assays (Verhaegen et al., 2002). Gaussia luciferase is a 20 kDa protein that oxidises coelenterazine in a rapid reaction resulting in a bright light emission at 470 nm.

Luciferases useful for the present invention have also been characterized from Anachnocampa sp (WO 2007/019634). These enzymes are about 59 kDa in size and are ATP-dependent luciferases that catalyse luminescence reactions with emission spectra within the blue portion of the spectrum.

Biologically active variants or fragments of naturally occurring bioluminescent protein can readily be produced by those skilled in the art. Three examples of such variants useful for the invention are RLuc2 (Loening et al., 2006), RLuc8 (Loening et al., 2006) and RLuc8.6-535 (Loening et al., 2007) which are each variants of Renilla luciferase. In a further preferred embodiment, the sequence of the BRET chemiluminescent donor is chosen to have greater thermal stability than sensor molecules incorporating native Renilla luciferase sensors. RLuc2 or RLuc8 are convenient examples of suitable choices, which consequently exhibit ≥5× or ≥10× higher luminance than sensors incorporating the native Renilla luciferase sequence. Such enhanced luminance has significant benefits as it permits more economical use of reagents for any given time resolution.

Alternative, non-luciferase, bioluminescent proteins that can be employed in this invention are any enzymes which can act on suitable substrates to generate a luminescent signal. Specific examples of such enzymes are β-galactosidase, lactamase, horseradish peroxidase, alkaline phosphatase, β-glucuronidase and β-glucosidase. Synthetic luminescent substrates for these enzymes are well known in the art and are commercially available from companies, such as Tropix Inc. (Bedford, Mass., USA).

An example of a peroxidase useful for the present invention is described by Hushpulian et al., (2007).

In some embodiments, the bioluminescent protein is a luciferase, a (β-galactosidase, a lactamase, a horseradish peroxidase, an alkaline phosphatase, a β-glucuronidase or a β-glucosidase. In some embodiments, the bioluminescent protein is luciferase. Suitable luciferase include, but are not limited to a Renilla luciferase, a Firefly luciferase (e.g. PpyRE8, PpyRE10), a Coelenterate luciferase, a North American glow worm luciferase, a click beetle luciferase, a railroad worm luciferase, a bacterial luciferase, a Gaussia luciferase, Aequorin, an Arachnocampa luciferase, an Oplophorus gracilirostris luciferase or a biologically active variant or fragment of any one, or chimera of two or more, thereof. In one example, the preferred luciferase is RLuc8 or a variant thereof.

As used herein, a “biologically active fragment” is a portion of a polypeptide as described herein which maintains a defined activity of the full-length polypeptide. As used herein, a “biologically active variant” is a molecule which differs from a naturally occurring and/or defined molecule by one or more amino acids but maintains a defined activity, such as defined above for biologically active fragments. Biologically active variants are typically least 50%, more preferably at least 80%, more preferably at least 90%, more preferably at least 95%, more preferably at least 97%, and even more preferably at least 99% identical to the naturally occurring and/or defined molecule.

In a preferred embodiment, a bioluminescent protein with a small molecular weight is used to prevent an inhibition of the interaction due to steric hindrance. The bioluminescent protein preferably consists of a single polypeptide chain. Also the bioluminescent proteins preferably do not form oligomers or aggregates. The bioluminescent proteins Renilla luciferase, Gaussia luciferase and Firefly luciferase meet all or most of these criteria.

In some embodiments, the chemiluminescent donor domain is capable of modifying a substrate. As used herein, the term “substrate” refers to any molecule that can be used in conjunction with a chemiluminescent donor to generate or absorb luminescence. The choice of the substrate can impact on the wavelength and the intensity of the light generated by the chemiluminescent donor. In some embodiments, the bioluminescent protein has a substrate selected from luciferin, calcium, coelenterazine, furimazine or a derivative, analogue or stabilised derivative of coelenterazine, luciferin or furimazine.

Coelenterazine is a widely known substrate which occurs in cnidarians, copepods, chaetognaths, ctenophores, decapod shrimps, mysid shrimps, radiolarians and some fish taxa (Greer and Szalay, 2002). For Renilla luciferase for example, coelenterazine analogues/derivatives are available that result in light emission between 418 and 547 nm (Inouye et al., 1997, Loening et al., 2007). A coelenterazine analogue/derivative (400A, DeepBlueC) has been described emitting light at 400 nm with Renilla luciferase (WO 01/46691). Other examples of coelenterazine analogues/derivatives are EnduRen, Prolume purple, Prolume purple II, Prolume purple III, ViviRen and Furimazine. Other examples of coelenterazine analogues/derivatives include, but are not limited to, compounds disclosed in PCT/US2013057660 and US20140302539.

As used herein, the term “luciferin” is defined broadly and refers to a class of light-emitting biological pigments found in organisms capable of bioluminescence as well as synthetic analogues or functionally equivalent chemicals, which are oxidised in the presence of the enzyme luciferase to produce oxyluciferin and energy in the form of light. D-luciferin, or 2-(6-hydroxybenzothiazol-2-yl)-2-thiazoline-4-carboxylic acid, was first isolated from the firefly Photinus pyralis. Since then, various chemically distinct forms of luciferin have been discovered and studied from various different organisms, mainly from the ocean, for example fish and squid, however, many have been identified in land dwelling organisms, for example, worms, beetles and various other insects (Day et al., 2004; Viviani, 2002). As used herein, luciferin also includes derivatives or analogues of luciferin.

In addition to entirely synthetic luciferin, such as cyclic alkylaminoluciferin (CycLuc1), there are at least five general types of biologically evolved luciferin, which are each chemically different and catalysed by chemically and structurally different luciferases that employ a wide range of different cofactors. First, is firefly luciferin, the substrate of firefly luciferase, which requires ATP for catalysis (EC 1.13.12.7). Second, is bacterial luciferin, also found in some squid and fish, that consists of a long chain aldehyde and a reduced riboflavin phosphate. Bacterial luciferase is FMNH-dependent. Third, is dinoflagellate luciferin, a tetrapyrrolic chlorophyll derivative found in dinoflagellates (marine plankton), the organisms responsible for night-time ocean phosphorescence. Dinoflagellate luciferase catalyses the oxidation of dinoflagellate luciferin and consists of three identical and catalytically active domains. Fourth, is the imidazolopyrazine vargulin, which is found in certain ostracods and deep-sea fish, for example, Porichthys. Last, is coelenterazine (an imidazolpyrazine), the light-emitter of the protein Aequorin, found in radiolarians, ctenophores, cnidarians, squid, copepods, chaetognaths, fish and shrimp.

In some embodiments, the bioluminescent protein requires a co-factor. Examples of co-factors include, but are not necessarily limited to, ATP, magnesium, oxygen, FMNH₂, calcium, or a combination of any two or more thereof.

In a further embodiment, the resonance energy transfer donor domain is a fluorescent donor domain. The fluorescent donor domain can be a fluorescent protein or a non-protein. In some embodiments, the fluorescent donor domain is a non-protein. Non-limiting examples of fluorophores that are suitable for use as the donor domain include, but are not limited to, Alexa Fluor dye (e.g. AF680, AF750), Bodipy dye, Cy dye, fluorescein, dansyl, umbelliferone, fluorescent microsphere, luminescent microsphere, fluorescent nanocrystal, Marina Blue, Cascade Blue, Cascade Yellow, Pacific Blue, Oregon Green, Tetramethylrhodamine, Rhodamine, Texas Red, rare earth element chelates, or any combination or derivatives thereof.

In some embodiments the donor domain is a fluorescent protein. Non-limiting examples include proteins such as green fluorescent protein (GFP), blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Venus, mOrange, Topaz, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), HcRed, t-HcRed, DsRed, DsRed2, t-dimer2, t-dimer2(12), mRFP1, pocilloporin, Renilla GFP, Monster GFP, paGFP, TdTomato, mCherry, Kaede protein, TagRFP, TurBoFB or a Phycobiliprotein, or a biologically active variant or fragment of any one thereof. In some embodiments, the preferred fluorescent donor domain is CFP.

B. Acceptor Domain

The sensor molecules of the present disclosure also comprise an acceptor domain. The acceptor domain is capable of serving as an acceptor domain in a resonance energy transfer pair (for example, in a BRET pair or a FRET pair) and, depending on context, is also referred to herein as a “resonance energy transfer acceptor domain”. As used herein, an “acceptor domain” is any molecule that is capable of accepting energy emitted as a result of the activity of the donor domain.

In some embodiments, the acceptor domain (also referred to herein as “acceptor molecule”) is a fluorescent acceptor domain. As used herein, the term “fluorescent acceptor domain” (also referred herein to as “fluorescent acceptor molecule”) refers to any compound which can accept energy emitted as a result of the activity of a donor domain, and re-emit it as light energy.

There are a number of different acceptor domains that can be employed in this invention. Suitable acceptor domains may be a protein or non-proteinaceous.

In some embodiments, the fluorescent acceptor domain is a fluorescent protein. One very well-known example is the group of fluorophores that includes the green fluorescent protein from the jellyfish Aequorea victoria and numerous other variants (GFPs) arising from the application of molecular biology, for example mutagenesis and chimeric protein technologies (Tsien, 1998). GFPs are classified based on the distinctive component of their chromophores, each class having distinct excitation and emission wavelengths: class 1, wild-type mixture of neutral phenol and anionic phenolate: class 2, phenolate anion: class 3, neutral phenol: class 4, phenolate anion with stacked s-electron system: class 5, indole: class 6, imidazole: and class 7, phenyl.

A naturally occurring acceptor molecule which has been mutated (variants) can also be useful for the present invention. One example of an engineered system which is suitable for BRET is a Renilla luciferase and enhanced yellow mutant of GFP (EYFP) pairing which do not directly interact to a significant degree with one another alone in the absence of a mediating protein(s) (in this case, the G protein coupled receptor) (Xu et al., 1999).

Examples include, but are not limited to, green fluorescent protein (GFP), blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Venus, mOrange, Topaz, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), HcRed, t-HcRed, DsRed, DsRed2, t-dimer2, t-dimer2(12), mRFP1, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein, TdTomato, mCherry, TagRFP, TurBoFB or a Phycobiliprotein, or a biologically active variant or fragment of any one thereof. In some embodiments, the preferred fluorescent acceptor domain is GFP². In other embodiments, the preferred fluorescent acceptor domain is YFP.

In some embodiments, the fluorescent acceptor domain is a non-protein. Examples of acceptor molecules that are not proteins include, but are not limited to, Alexa Fluor dye (e.g. AF680, AF750), Bodipy dye, Cy dye, fluorescein, dansyl, umbelliferone, fluorescent microsphere, luminescent microsphere, fluorescent nanocrystal, Marina Blue, Cascade Blue, Cascade Yellow, Pacific Blue, Oregon Green, Tetramethylrhodamine, Rhodamine, Texas Red, rare earth element chelates, or any combination or derivatives thereof.

C. Donor Domain and Acceptor Domain Pairs

Any number of donor-acceptor combinations can be used in the sensors of the present invention. The donor-acceptor combination should be capable of serving as a BRET pair or a FRET pair. A worker skilled in the art would be able to select a donor and acceptor pair which permits efficient energy transfer.

In preferred embodiments, the separation and relative orientation of the donor domain and the acceptor domain, in the presence and/or absence of the carbohydrate, is within ±50% of the Förster distance. As used herein, the term “the separation and relative orientation of the donor domain and the acceptor domain, in the presence and/or the absence of carbohydrate, is within ±50% of the Förster distance” refers to the steady state RET measurements which can be carried out within a range of ±50% of Ro. This phrase encompasses an efficiency of luminescence energy transfer from the donor domain to the acceptor domain in the range of 10-90%. In some embodiments, the Förster distance of the chemiluminescent donor domain and the acceptor domain is at least 4 nm, is at least 5.6 nm, or is at least 6 nm. In some embodiments, the Förster distance is less than 12 nm, less than 11 nm, less than 10 nm or less than 9 nm. In some embodiments, the Förster distance of the donor domain and the acceptor domain is between about 4 nm and about 11 nm, is between about 5.6 nm and about 11 nm or is between about 7 nm and about 11 nm. Without wishing to be bound by theory, the inventors believe that the Förster distance of the donor domain and the acceptor domain matches the size of the carbohydrate binding domain useful in the sensors of the present application. The carbohydrate binding domain may be, for example, a full length HTH transcription factor, a fragment thereof that retains carbohydrate binding activity, a carbohydrate binding domain of a HTH transcription factor, or a variant thereof.

A criterion which should be considered in determining suitable pairings is the relative emission/fluorescence spectrum of the acceptor molecule compared to that of the donor. The emission spectrum of the donor should overlap with the absorbance spectrum of the acceptor molecule such that the light energy from the donor emission is at a wavelength that is able to excite the acceptor molecule and thereby promote acceptor molecule fluorescence when the two molecules are in a proper proximity and orientation with respect to one another. For example, it has been demonstrated that a Renilla luciferase/EGFP pairing is not as good as a Renilla luciferase/EYEF pairing based on observable emission spectral peaks (Xu et al., 1999; Wang et al., (1997) in Bioluminescence and Chemiluminescence: Molecular Reporting with Photons, eds. Hastings et al., (Wiley, New York), pp. 419-422). To study potential pairing, protein fusions (for example) are prepared containing the selected donor and acceptor domains and are tested, in the presence of an appropriate substrate if required.

It should also be confirmed that the donor and acceptor domains do not spuriously associate with each other. For example, this can be accomplished by separate co-expression of a bioluminescent protein and acceptor molecule in the same cells and then monitoring the luminescence spectrum in order to determine if BRET occurs. This may be achieved, for example, using the method of Xu et al., (1999). The selected bioluminescent protein and acceptor molecule form a suitable BRET pair if little or no BRET is observed. Similar experiments can be performed for FRET pairs.

In some embodiments, the sensor molecules of the present disclosure comprise a chemiluminescent donor domain and fluorescent acceptor domain.

In some embodiments, the donor emission can be manipulated by modifications to the substrate. In the case of Renilla luciferases the substrate is coelenterazine. The rationale behind altering the donor emission is to improve the resolution between donor emission and acceptor emissions. The original BRET system uses the Renilla luciferase as donor, EYFP (or Topaz) as the acceptor and coelenterazine h derivative as the substrate. These components when combined in a BRET assay, generate light in the 475-480 nm range for the bioluminescent protein and the 525-530 nm range for the acceptor molecule, giving a spectral resolution of 45-55 nm.

Unfortunately, Renilla luciferase generates a broad emission peak overlapping substantially the GFP emission, which in turn contributes to decrease the signal to noise of the system. One BRET system for use in the present invention has coel400a as the Renilla luciferase substrate and provides broad spectral resolution between donor and acceptor emission wavelengths (˜105 nm). Renilla luciferase with coe400a generates light between 390-400 nm and a GFP derivative (GFP²) was prepared which absorbs light in this range and re-emits light at 505-508 nm. Because of this increase in spectral resolution between Renilla luciferase and GFP emissions, this BRET system provides an excellent biological tool to monitor binding of a carbohydrate to the sensors of the present application. However, smaller Stokes shift BRET systems would also allow sensitive measurement of carbohydrates.

Various coelenterazine derivatives are known in the art, including coel400a, that generate light at various wavelengths (distinct from that generated by the wild type coelenterazine) as a result of Renilla luciferase activity. A worker skilled in the art would appreciate that because the light emission peak of the donor has changed, it is necessary to select an acceptor molecule which will absorb light at this wavelength and thereby permit efficient energy transfer. This can be done, for example by altering a GFP class 4 such that it becomes a class 3 or 1 GFP. Spectral overlapping between light emission of the donor and the light absorption peak of the acceptor is one condition among others for an efficient energy transfer. Class 3 and 1 GFPs are known to absorb light at 400 nm and re-emit between 505-511 nm. This results in a wavelength difference between donor and acceptor emissions of approximately 111 nm.

Examples of further bioluminescent protein and acceptor molecule pairs are provided in Table 3.

TABLE 3 Exemplary BRET bioluminescent proteins and acceptor molecule pairs. Substrate Fluorescence Wavelength of BDP Substrate wavelength (peak) acceptor molecule acceptor (Ex/Em) RLuc2 Native 470 nm Venus 515/528 nm RLuc8 coelenterazine RLuc2 Native 470 nm mOrange 548/562 nm RLuc8 coelenterazine RLuc2 Native 470 nm EYFP/Topaz 514/527 nm RLuc8 Coelenterazine RLuc2 Native 470 nm mCitrine 516/529 nm RLuc8 Coelenterazine RLuc Native 470 nm YPet 517/530 nm RLuc2 Coelenterazine RLuc8 RLuc2 Native 470 nm Fluorescein 495/519 nm RLuc8 Coelenterazine RLuc2 Native 470 nm Acridine yellow 470/550 nm RLuc8 Coelenterazine RLuc2 Native 470 nm Nile red 485/525 nm RLuc8 Coelenterazine RLuc2 Native 470 nm R-Phycoerythrin 480/578 nm RLuc8 Coelenterazine RLuc2 Native 470 nm Red 613 480/613 nm RLuc8 Coelenterazine RLuc2 Native 470 nm TruRed 490/695 nm RLuc8 Coelenterazine RLuc8.6-5.35 Native 535 nm mOrange 548/562 nm Coelenterazine RLuc8.6-5.35 Coelenterazine h 535 nm TagRFP 555/584 nm RLuc8.6-5.35 Coelenterazine h 535 nm TurboRFP 588/635 nm RLuc Coelenterazine v 515 nm mOrange 548/562 nm RLuc2 RLuc8 RLuc Coelenterazine v 515 nm TagRFP 555/584 nm RLuc2 RLuc8 RLuc8.6-5.35 Coelenterazine v 570 nm TurboRFP 588/635 nm RLuc2 Coelenterazine h 470 nm Venus 515/528 nm RLuc8 RLuc2 Coelenterazine h 470 nm mOrange 548/528 nm RLuc8 RLuc2 Coelenterazine h 470 nm EYFP/Topaz 514/527 nm RLuc8 RLuc2 Coelenterazine h 470 nm mCitrine 516/529 nm RLuc8 RLuc2 Native 470 nm YPet 517/530 nm RLuc8 Coelenterazine RLuc Coelenterazine h 470 nm Fluorescein 490/525 nm RLuc2 RLuc8 RLuc Coelenterazine h 470 nm Acridine yellow 470/550 nm RLuc2 RLuc8 RLuc Coelenterazine h 470 nm Nile red 485/525 nm RLuc2 RLuc8 RLuc Coelenterazine h 470 nm R-Phycoerythrin 480/578 nm RLuc2 RLuc8 RLuc Coelenterazine h 470 nm Red 613 480/613 nm RLuc2 RLuc8 RLuc Coelenterazine h 470 nm TruRed 490/695 nm RLuc2 RLuc8 RLuc8.6-5.35 Coelenterazine h 535 nm mOrange 548/562 nm RLuc Coelenterazine 400a 400 nm GFP² 396/508 nm RLuc2 RLuc8 RLuc Coelenterazine 400a 400 nm GFP10 400/510 nm RLuc2 RLuc8 RLuc Coelenterazine 400a 400 nm Wild type GFP 396 (475)/508 nm RLuc2 RLuc8 RLuc Coelenterazine 400a 400 nm TagBFP 402/457 nm RLuc2 RLuc8 RLuc Coelenterazine 400a 400 nm Cerulean/mCFP 433/475 nm RLuc2 RLuc8 RLuc Coelenterazine 400a 400 nm ECFP/CyPet 434/477 nm RLuc2 RLuc8 RLuc Coelenterazine 400a 400 nm Y66W 436/485 nm RLuc2 RLuc8 RLuc Coelenterazine 400a 400 nm dKeima-Red 440/616 nm RLuc2 RLuc8 RLuc Coelenterazine 400a 400 nm mKeima-Red 440/620 nm RLuc2 RLuc8 RLuc Coelenterazine 400a 400 nm Quin-2 365/490 nm RLuc2 RLuc8 RLuc Coelenterazine 400a 400 nm Pacific blue 403/551 nm RLuc2 RLuc8 RLuc Coelenterazine 400 400 nm Dansychloride 380/475 nm RLuc2 RLuc8 Firefly Luciferin 560 nm Cyanine Cy3 575/605 nm luciferase Firefly Luciferin 560 nm Texas red 590/615 nm luciferase Firefly Luciferin 560 nm TurboRed 553/574 nm luciferase Firefly Luciferin 560 nm tdTomato 554/581 nm luciferase Firefly Luciferin 560 nm TagRFP 555/584 nm luciferase Firefly Luciferin 560 nm DsRed 557/592 nm luciferase Firefly Luciferin 560 nm mRFP1 584/607 nm luciferase Firefly Luciferin 560 nm mCherry 587/610 nm luciferase Beetle green Luciferin 560 nm tdTomato 554/581 nm luciferase FFLuc Luciferin 560 nm AF680 679/702 nm PpyRE8 PpyRE10 FFLuc Luciferin 560 nm AF750 749/775 nm PpyRE8 PpyRE10 NanoLuc Furimazine 460 nm Venus 515/528 nm NanoLuc Furimazine 460 nm mOrange 548/562 nm NanoLuc Furimazine 460 nm EYFP/Topaz 514/527 nm NanoLuc Furimazine 460 nm mCitrine 516/529 nm NanoLuc Furimazine 460 nm YPet 517/530 nm NanoLuc Furimazine 460 nm Fluorescein 495/519 nm NanoLuc Furimazine 460 nm Acridine yellow 470/550 nm NanoLuc Furimazine 460 nm Nile red 485/525 nm NanoLuc Furimazine 460 nm R-Phycoerythrin 480/487 nm NanoLuc Furimazine 460 nm Red 613 480/613 nm NanoLuc Furimazine 460 nm TruRed 490/695 nm NanoLuc Furimazine 460 nm Oregon Green 496/516 nm NanoLuc Furimazine 460 nm diAcFAM 494/526 nm NanoLuc Furimazine 460 nm AlexFluor488 494/517 nm NanoLuc Furimazine 460 nm TMR 555/585 nm NanoLuc Furimazine 460 nm Halotag NCT 595/635 nm NanoLuc Furimazine 460 nm HalotagBRET 618 525/618 nm NanoLuc Native 460 nm Venus 515/528 nm Coelenterazine NanoLuc Native 460 nm mOrange 548/562 nm Coelenterazine NanoLuc Native 460 nm EYFP/Topaz 514/527 nm Coelenterazine NanoLuc Native 460 nm mCitrine 516/529 nm Coelenterazine NanoLuc Native 460 nm YPet 517/530 nm Coelenterazine NanoLuc Native 460 nm Fluorescein 495/519 nm Coelenterazine NanoLuc Native 460 nm Acridine yellow 470/550 nm Coelenterazine NanoLuc Native 460 nm Nile red 485/525 nm Coelenterazine NanoLuc Native 460 nm R-Phycoerythrin 480/487 nm Coelenterazine NanoLuc Native 460 nm Red 613 480/613 nm Coelenterazine NanoLuc Native 460 nm TruRed 490/695 nm Coelenterazine NanoLuc Native 460 nm Oregon Green 496/516 nm Coelenterazine NanoLuc Native 460 nm diAcFAM 494/526 nm Coelenterazine NanoLuc Native 460 nm AlexFluor488 494/517 nm Coelenterazine NanoLuc Native 460 nm TMR 555/585 nm Coelenterazine NanoLuc Native 460 nm Halotag NCT 595/635 nm Coelenterazine NanoLuc Native 460 nm HalotagBRET 618 525/618 Coelenterazine NanoLuc Native 460 nm Oregon Green 496/516 nm Coelenterazine NanoLuc Native 460 nm diAcFAM 494/526 nm Coelenterazine NanoLuc Native 460 nm AlexFluor488 494/517 nm Coelenterazine NanoLuc Native 460 nm TMR 555/585 nm Coelenterazine NanoLuc Native 460 nm Halotag NCT 595/635 nm Coelenterazine NanoLuc Native 460 nm HalotagBRET 618 525/618 Coelenterazine NanoLuc Coelenterazine h 460 nm Venus 515/528 nm NanoLuc Coelenterazine h 460 nm mOrange 548/562 nm NanoLuc Coelenterazine h 460 nm EYFP/Topaz 514/527 nm NanoLuc Coelenterazine h 460 nm mCitrine 516/529 nm NanoLuc Coelenterazine h 460 nm YPet 517/530 nm NanoLuc Coelenterazine h 460 nm Fluorescein 495/519 nm NanoLuc Coelenterazine h 460 nm Acridine yellow 470/550 nm NanoLuc Coelenterazine h 460 nm Nile red 485/525 nm NanoLuc Coelenterazine h 460 nm R-Phycoerythrin 480/487 nm NanoLuc Coelenterazine h 460 nm Red 613 480/613 nm NanoLuc Coelenterazine h 460 nm TruRed 490/695 nm NanoLuc Coelenterazine h 460 nm Oregon Green 496/516 nm NanoLuc Coelenterazine h 460 nm diAcFAM 494/526 nm NanoLuc Coelenterazine h 460 nm AlexFluor488 494/517 nm NanoLuc Coelenterazine h 460 nm TMR 555/585 nm NanoLuc Coelenterazine h 460 nm Halotag NCT 595/635 nm NanoLuc Coelenterazine h 460 nm HalotagBRET 618 525/618 RLuc Prolume Purple 405 nm GFP² 396/508 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 405 nm GFP10 400/510 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 405 nm Wild type GFP 396 (475)/508 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 405 nm TagBFP 402/457 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 405 nm Cerulean/mCFP 433/475 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 405 nm ECFP/CyPet 434/477 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 405 nm Y66W 436/485 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 405 nm dKeima-Red 440/616 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 405 nm mKeima-Red 440/620 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 405 nm Quin-2 365/490 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 405 nm Pacific blue 403/551 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 405 nm Dansychloride 380/475 nm RLuc2 Substrate RLuc8 RLuc Prolume Purple 400 nm GFP² 396/508 nm RLuc2 Substrate II RLuc8 RLuc Prolume Purple 400 nm GFP10 400/510 nm RLuc2 Substrate II RLuc8 RLuc Prolume Purple 400 nm Wild type GFP 396 (475)/508 nm RLuc2 Substrate II RLuc8 RLuc Prolume Purple 400 nm TagBFP 402/457 nm RLuc2 Substrate II RLuc8 RLuc Prolume Purple 400 nm Cerulean/mCFP 433/475 nm RLuc2 Substrate II RLuc8 RLuc Prolume Purple 400 nm ECFP/CyPet 434/477 nm RLuc2 Substrate II RLuc8 RLuc Prolume Purple 400 nm Y66W 436/485 nm RLuc2 Substrate II RLuc8 RLuc Prolume Purple 400 nm dKeima-Red 440/616 nm RLuc2 Substrate II RLuc8 RLuc Prolume Purple 400 nm mKeima-Red 440/620 nm RLuc2 Substrate II RLuc8 RLuc Prolume Purple 400 nm Quin-2 365/490 nm RLuc2 Substrate II RLuc8 RLuc Prolume Purple 400 nm Pacific blue 403/551 nm RLuc2 Substrate II RLuc8 RLuc Prolume Purple 400 nm Dansychloride 380/475 nm RLuc2 Substrate II RLuc Prolume Purple 410 nm GFP² 396/508 nm RLuc2 Substrate III RLuc8 RLuc Prolume Purple 410 nm GFP10 400/510 nm RLuc2 Substrate III RLuc8 RLuc Prolume Purple 410 nm Wild type GFP 396 (475)/508 nm RLuc2 Substrate III RLuc8 RLuc Prolume Purple 410 nm TagBFP 402/457 nm RLuc2 Substrate III RLuc8 RLuc Prolume Purple 410 nm Cerulean/mCFP 433/475 nm RLuc2 Substrate III RLuc8 RLuc Prolume Purple 410 nm ECFP/CyPet 434/477 nm RLuc2 Substrate III RLuc8 RLuc Prolume Purple 410 nm Y66W 436/485 nm RLuc2 Substrate III RLuc8 RLuc Prolume Purple 410 nm dKeima-Red 440/616 nm RLuc2 Substrate III RLuc8 RLuc Prolume Purple 410 nm mKeima-Red 440/620 nm RLuc2 Substrate III RLuc8 RLuc Prolume Purple 410 nm Quin-2 365/490 nm RLuc2 Substrate III RLuc8 RLuc Prolume Purple 410 nm Pacific blue 403/551 nm RLuc2 Substrate III RLuc8 RLuc Prolume Purple 410 nm Dansychloride 380/475 nm RLuc2 Substrate III RLuc8

In some embodiments, the preferred bioluminescent protein and acceptor domain pair is RLuc8 and GFP².

In some embodiments, the sensor molecules of the present disclosure comprise a fluorescent donor domain and a fluorescent acceptor domain.

Any appropriately selected fluorophore can be used as the donor and/or acceptor, provided that the emission spectrum of the donor overlaps sufficiently with the excitation spectrum of the acceptor. A criterion which should be considered in determining suitable pairings is the excitation spectrum of the acceptor molecule compared to that of the donor. As the person skilled in the art would appreciate there should be minimum direct excitation of the acceptor domain at the excitation maximum of the donor domain.

Examples of further fluorescent donor and acceptor domain pairs are provided in Table 4. Other examples of fluorescent donor and acceptor domain pairs are discussed in Bajar et al. (2016).

TABLE 4 Exemplary FRET fluorescent donor and acceptor domain pairs. Wavelength Fluorescence Wavelength Fluorescent of accentor acceptor of acceptor donor (Em) molecule (Exc) FITC 520 nm TRITC 550 nm Cy3 566 nm Cy5 649 nm EGFP 508 nm Cy3 554 nm CFP 477 nm YEP 514 nm EGFP 508 nm YFP 514 nm GFP² YFP 514 nm ECFP 475 nm EYFP 513 nm mTurquioise2 474 nm mCitrine 516 nm mClover3 518 nm mRuby3 558 nm eqFP650 650 nm iRFP 690 nm mAmetrine 526 nm tdTomato 554 nm

In some embodiments, the preferred donor domain and acceptor domain pair is CFP and YFP.

Carbohydrate Binding

Binding of a carbohydrate to the carbohydrate binding domain of the sensors of the present disclosure alters the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain. In some embodiments, the alteration in spatial location and/or dipole orientation results in a change in BRET. In some embodiments, the alteration in spatial location and/or dipole orientation results in a change in FRET.

As used herein, the term “spatial location” refers to the three dimensional positioning of the donor relative to the acceptor molecule which changes as a result of the analyte binding or releasing from the sensor molecule.

As used herein, the term “dipole orientation” refers to the direction in three-dimensional space of the dipole moment associated either with the donor and/or the acceptor molecule relative their orientation in three-dimensional space. The dipole moment is a consequence of a variation in electrical charge over a molecule.

Using BRET as an example, in an embodiment the energy transfer occurring between the bioluminescent protein and acceptor molecule is presented as calculated ratios from the emissions measured using optical filters (one for the acceptor molecule emission and the other for the bioluminescent protein emission) that select specific wavelengths (see equation 1).

E _(a) /E _(d)=BRET ratio  (1)

where E_(a) is defined as the acceptor molecule emission intensity (emission light is selected using a specific filter adapted for the emission of the acceptor) and E_(d) is defined as the bioluminescent protein emission intensity (emission light is selected using a specific filter adapted for the emission of the bioluminescent protein).

It should be readily appreciated by those skilled in the art that the optical filters may be any type of filter that permits wavelength discrimination suitable for BRET. For example, optical filters used in accordance with the present invention can be interference filters, long pass filters, short pass filters, etc. Intensities (usually in counts per second (CPS) or relative luminescence units (RLU)) of the wavelengths passing through filters can be quantified using either a photo-multiplier tube (PMT), photodiode, including a cascade photodiode, photodiode array or a sensitive camera such as a charge coupled device (CCD) camera. The quantified signals are subsequently used to calculate BRET ratios and represent energy transfer efficiency. The BRET ratio increases with increasing intensity of the acceptor emission.

Generally, a ratio of the acceptor emission intensity over the donor emission intensity is determined (see equation 1), which is a number expressed in arbitrary units that reflects energy transfer efficiency. The ratio increases with an increase of energy transfer efficiency (see Xu et al., 1999).

Energy transfer efficiencies can also be represented using the inverse ratio of donor emission intensity over acceptor emission intensity (see equation 2). In this case, ratios decrease with increasing energy transfer efficiency. Prior to performing this calculation the emission intensities are corrected for the presence of background light and auto-luminescence of the substrate. This correction is generally made by subtracting the emission intensity, measured at the appropriate wavelength, from a control sample containing the substrate but no bioluminescent protein, acceptor molecule or polypeptide of the invention.

E _(d) /E _(a)=BRET ratio  (2)

where E_(a) and E_(d) are as defined above.

The light intensity of the bioluminescent protein and acceptor molecule emission can also be quantified using a monochromator-based instrument such as a spectrofluorometer, a charged coupled device (CCD) camera or a diode array detector. Using a spectrofluorometer, the emission scan is performed such that both bioluminescent protein and acceptor molecule emission peaks are detected upon addition of the substrate. The areas under the peaks represent the relative light intensities and are used to calculate the ratios, as outlined above. Any instrument capable of measuring lights for the bioluminescent protein and acceptor molecule from the same sample, can be used to monitor the BRET system of the present invention.

In an alternative embodiment, the acceptor molecule emission alone is suitable for effective detection and/or quantification of BRET. In this case, the energy transfer efficiency is represented using only the acceptor emission intensity. It would be readily apparent to one skilled in the art that in order to measure energy transfer, one can use the acceptor emission intensity without making any ratio calculation. This is due to the fact that ideally the acceptor molecule will emit light only if it absorbs the light transferred from the bioluminescent protein. In this case only one light filter is necessary.

In a related embodiment, the bioluminescent protein emission alone is suitable for effective detection and/or quantification of BRET. In this case, the energy transfer efficiency is calculated using only the bioluminescent protein emission intensity. It would be readily apparent to one skilled in the art that in order to measure energy transfer, one can use the donor emission intensity without making any ratio calculation. This is due to the fact that as the acceptor molecule absorbs the light transferred from the bioluminescent protein there is a corresponding decrease in detectable emission from the bioluminescent protein. In this case only one light filter is necessary.

In an alternative embodiment, the energy transfer efficiency is represented using a ratiometric measurement which only requires one optical filter for the measurement. In this case, light intensity for the donor or the acceptor is determined using the appropriate optical filter and another measurement of the samples is made without the use of any filter (intensity of the open spectrum). In this latter measurement, total light output (for all wavelengths) is quantified. Ratio calculations are then made using either equation 3 or 4. For the equation 3, only the optical filter for the acceptor is required. For the equation 4, only the optical filter for the donor is required.

E _(a) /E _(o) −E _(a)=BRET ratio or=E _(o) −E _(a) /E _(a)  (3)

E _(o) −E _(d) /E _(d)=BRET ratio or=E _(d) /E _(o) −E _(d)  (4)

where E_(a) and E_(d) are as defined above and E_(o) is defined as the emission intensity for all wavelengths combined (open spectrum).

It should be readily apparent to one skilled in the art that further equations can be derived from equations 1 through 4. For example, one such derivative involves correcting for background light present at the emission wavelength for bioluminescent protein and/or acceptor molecule.

In performing a BRET assay, light emissions can be determined from each well using the BRETCount. The BRETCount instrument is a modified TopCount, wherein the TopCount is a microtiterplate scintillation and luminescence counter sold by Packard Instrument (Meriden, Conn.). Unlike classical counters which utilise two photomultiplier tubes (PMTs) in coincidence to eliminate background noise, TopCount employs single-PMT technology and time-resolved pulse counting for noise reduction to allow counting in standard opaque microtiter plates. The use of opaque microtiterplates can reduce optical crosstalk to negligible level. TopCount comes in various formats, including 1, 2, 6 and 12 detectors (PMTs), which allow simultaneous reading of 1, 2, 6 or 12 samples, respectively. Beside the BRETCount, other commercially available instruments are capable of performing BRET: the Victor 2 (Wallac, Finland (Perkin Elmer Life Sciences)) and the Fusion (Packard Instrument, Meriden). BRET can be performed using readers that can detect at least the acceptor molecule emission and preferably two wavelengths (for the acceptor molecule and the bioluminescent protein) or more.

BRET is a ratiometric technique which can eliminate data variability caused by fluctuations in light output due to variations in assay volume, assay conditions and signal decay across different wells in a plate. RET-based reactions are homogeneous, generally occurring in solution without solid-phase attachment. This allows for detection of analytes in different forms such as liquid, gas and even particulates without separation.

Lactose Sensor Molecule

One non-limiting example of a sensor molecule as defined herein is a sensor molecule that can used to detect and/or measure lactose concentration. Accordingly, in some embodiments the present disclosure provides a sensor molecule for detecting lactose comprising a bacterial transcription factor which is capable of binding lactose or variant thereof, covalently joined to a resonance energy transfer donor domain and a resonance energy transfer acceptor domain, wherein the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain is altered when lactose binds to the transcription factor. In some embodiments, the present disclosure provides a sensor molecule for detecting lactose comprising a bacterial BgaR transcription factor or variant thereof, covalently joined to a resonance energy transfer donor domain and a resonance energy transfer acceptor domain, wherein the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain is altered when lactose binds to the transcription factor. Binding of lactose to the sensor produces a change in resonance energy transfer (RET) such that a change in RET indicates lactose is present. Depending on the chosen donor domain and acceptor domain the change in RET can be a change in BRET or a change in FRET.

In some embodiments, the BgaR transcription factor or variant thereof has an amino acid sequence which is at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to that provided in SEQ ID NO: 1, or a sequence at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a portion thereof. In some embodiments, the BgaR transcription factor is 100% identical to that provided in SEQ ID NO: 1. In some embodiments, the BgaR transcription factor or variant thereof has an amino acid sequence which is at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to that provided in SEQ ID NO: 9. In some embodiments, the BgaR transcription factor or variant thereof is 100% identical to that provided in SEQ ID NO: 9.

In some embodiments, the resonance energy transfer donor domain is a bioluminescent protein. Non-limiting examples of suitable bioluminescent proteins are described hereinabove and include luciferase, a β-galactosidase, a lactamase, a horseradish peroxidase, an alkaline phosphatase, a β-glucuronidase or a β-glucosidase. In some embodiments, the bioluminescent protein is a luciferase. The luciferase can be selected from the group consisting of Renilla luciferase, a Firefly luciferase, a Coelenterate luciferase, a North American glow worm luciferase, a click beetle luciferase, a railroad worm luciferase, a bacterial luciferase, a Gaussia luciferase, Aequorin, an Arachnocampa luciferase, and an Oplophorus gracilirostris luciferase or a biologically active variant or fragment of any one, or chimera of two or more, thereof. In some embodiments, the resonance energy transfer donor domain is a Renilla luciferase. In some embodiments, the resonance energy transfer donor domain is RLuc8. In some embodiments, the resonance energy transfer donor domain is capable of modifying a substrate. Non-limiting examples of substrates include luciferin, calcium, coelenterazine, furimazine or a derivative, analogue or stabilised derivative of coelenterazine, luciferin or furimazine. In these embodiments, binding of lactose to the sensor molecule results in a change in BRET.

In alternative embodiments, the resonance energy transfer donor domain is a fluorescent protein. Non-limiting examples of suitable fluorescent proteins include green fluorescent protein (GFP), blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Venus, mOrange, Topaz, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), HcRed, t-HcRed, DsRed, DsRed2, t-dimer2, tdimer2(12), mRFP1, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein, tdTomato, mCherry, TagRFP, TurBoFB and a Phycobiliprotein, and a biologically active variant or fragment of any one thereof. In some embodiments, the donor domain is CFP. In these embodiments, binding of lactose to the sensor molecule results in a change in FRET.

In some embodiments, the resonance energy transfer acceptor domain is a fluorescent acceptor domain. In some embodiments, the fluorescent acceptor domain is a fluorescent protein. Non-limiting examples of suitable fluorescent proteins include green fluorescent protein (GFP), blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Venus, mOrange, Topaz, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), HcRed, t-HcRed, DsRed, DsRed2, t-dimer2, tdimer2(12), mRFP1, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein, tdTomato, mCherry, TagRFP, TurBoFB and a Phycobiliprotein, and a biologically active variant or fragment of any one thereof. In some embodiments, the acceptor domain is YFP. In other embodiments, the acceptor domain is GFP, preferably GFP².

In preferred embodiments, the donor domain is CFP or a variant thereof and the acceptor domain is YFP or a variant thereof. In some embodiments, the sensor further comprises a linker between YFP and BgaR and/or between CFP and BgaR. In some embodiments, the sensor further comprises protease cleavage sites and/or purification tags. In some embodiments, the sensor comprises an amino acid sequence which is at least 30% identical, at least 35% identical, at least 40% identical, at least 45% identical, at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, at least 99.5% identical to the amino acid sequence provided in SEQ ID NO: 23. In some embodiments, the sensor is 100% identical to that provided in SEQ ID NO: 23. In these embodiments, binding of lactose to the sensor molecule results in a change in FRET.

In other preferred embodiments, the donor domain is Renilla luciferase or a variant thereof and the acceptor domain is GFP or a variant thereof. For example, the donor domain can be RLuc8 and the acceptor domain can be GFP². In some embodiments, the sensor molecule is a single polypeptide comprising RLuc8-BgaR-GFP². In some embodiments, the sensor molecule is a single polypeptide comprising GFP²-BgaR-RLuc8. In some embodiments, the sensor further comprises a linker between GFP² and BgaR and/or between RLuc8 and BgaR. In some embodiments, the sensor further comprises protease cleavage sites and/or purification tags. In some embodiments, the sensor comprises an amino acid sequence which is at least 30% identical, at least 35% identical, at least 40% identical, at least 45% identical, at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, at least 99.5% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28. In some embodiments, the sensor comprises an amino acid sequence which is at least 30% identical, at least 35% identical, at least 40% identical, at least 45% identical, at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, at least 99.5% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35 and SEQ ID NO: 36. In some embodiments, the sensor comprises an amino acid sequence which is at least 30% identical, at least 35% identical, at least 40% identical, at least 45% identical, at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, at least 99.5% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18. In some embodiments, the sensor comprises an amino acid sequence which is at least 30% identical, at least 35% identical, at least 40% identical, at least 45% identical, at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, at least 99.5% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28. In some embodiments, the sensor has an amino acid sequence which is 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28. In some embodiments, the sensor has an amino acid sequence which is 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18. In some embodiments, the sensor has an amino acid sequence which is 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28. In some embodiments, the sensor has an amino acid sequence which is 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35 and SEQ ID NO: 36. In some embodiments, the sensor comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28 or is a fragment or variant thereof. In some embodiments, the sensor comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18 or is a fragment or variant thereof. In some embodiments, the sensor comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28 or is a fragment or variant thereof. In these embodiments, binding of lactose to the sensor molecule results in a change in BRET.

A sensor molecule that can be used to detect and/or measure lactose concentration is of particular interest for use in determining residual lactose in lactose-free products. High levels of lactose (5%) are found in milk and milk products (cream, butter, ice cream, cheese, powdered milk) (Fernandes Silveira et al., 2015). There is a growing market for lactose-free and lactose-reduced products, but there is no cheap, fast, sensitive method to measure residual amounts of lactose in dairy following treatment to remove or reduce the amounts of lactose. According to Food Standards Australia New Zealand (FSANZ), lactose-reduced dairy products must contain no more than 0.3% lactose. Lactose-free products are defined as having undetectable levels of the disaccharide, a definition which is subject to interpretation. However, levels of lactose below 0.01% are required for the European and Chinese markets.

Although the enzymatic process leading to the reduction/elimination of lactose in milk is well established, there are no established means for those carrying out the enzymatic process to verify the degree of lactose reduction at the time of processing. Currently, lactose-reduced and lactose-free milk samples are sent away from the processing plant to specialised laboratories for analysis. This incurs additional costs, due to logistics, need for specialised laboratory equipment and expertise, and the need for additional holding of the goods being assessed. In addition to the costs associated with current analysis methods and storage, not all lactose-free milk is tested, leading to an uneven treatment of milk and potential unreliability of products for the consumer. Accordingly, there is a need for alternative methods and sensors for measuring the concentration of lactose in food products, for example lactose reduced and lactose free dairy products. Preferably, the methods and sensors would provide dairy processors with a fast, sensitive, selective, inline method for the measurement of low levels of lactose in milk at the processing plant.

Measurement of residual lactose in milk represents a challenge on at least two levels: i) the amount of lactose in milk following enzymatic treatment to degrade the lactose is approximately 0.01% w/v; ii) selectivity due to the presence of high concentrations of lactose-derived monosaccharides that might interfere with the measurement of lactose. Preferably, the methods and sensors described in some embodiments will be able to detect lactose at a concentration of approximately 0.0001% w/v or more, approximately 0.0003% w/v or more, approximately 0.0005% w/v or more, approximately 0.0007% w/v or more, approximately 0.001% w/v or more, approximately 0.003% w/v or more, approximately 0.005% w/v or more, approximately 0.007% w/v or more, approximately 0.01% w/v or more, approximately 0.03% w/v or more, approximately 0.05% w/v or more, approximately 0.07% w/v or more, or approximately 0.1% w/v or more. Preferably, the methods and sensors described in some embodiments will be able to detect lactose in the presence of other carbohydrates, for example lactose-derived monosaccharides and/or lactulose. In some embodiments, the methods and sensors described can detect lactose in the presence of at least 0.1 mM, at least 1 mM, at least 10 mM, at least 20 mM, at least 50 mM, at least 100 mM, at least 130 mM, at least 200 mM, at least 260 mM carbohydrate, at least 300 mM, or at least 350 mM total carbohydrate. As the person skilled in the art would understand, the total carbohydrate concentrations exclude lactose (for example, if the sample comprises lactose, galactose and glucose, the concentration refers to the concentration of glucose and galactose). In some embodiments, the methods and sensors described can detect lactose in the presence of at least 0.1 mM, at least 1 mM, at least 10 mM, at least 20 mM, at least 50 mM, at least 100 mM, at least 130 mM, at least 200 mM, at least 260 mM carbohydrate, at least 300 mM, or at least 350 mM glucose and galactose.

In some embodiments, there is provided a sensor molecule for detecting lactose, the sensor comprising

i) a lactose binding domain of a helix-turn-helix transcription factor, or a variant of the carbohydrate binding domain;

ii) a chemiluminescent donor domain; and

iii) an acceptor domain;

wherein the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain is altered when lactose binds to the carbohydrate binding domain.

In some embodiments, there is provided a sensor molecule for detecting lactose, the sensor comprising

i) a bacterial BgaR transcription factor;

ii) a resonance energy transfer donor domain; and

iii) a resonance energy transfer acceptor domain;

wherein the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain is altered when lactose binds to the transcription factor. The resonance energy transfer donor domain and resonance energy transfer acceptor domain are as defined herein.

Lactulose Sensor Molecule

A further non-limiting example of a sensor molecule as defined herein is a sensor molecule that can used to detect and/or measure lactulose concentration. Accordingly, in some embodiments the present disclosure provides a sensor molecule as defined herein for detecting lactulose. In some embodiments, the methods and sensors described herein will be able to detect lactulose at a concentration of approximately 0.05 mM or more, approximately 0.1 mM or more, approximately 0.5 mM or more, approximately 1 mM or more, approximately 1.5 mM or more, approximately 1.8 mM or more or approximately 2 mM or more. In some embodiments, the methods and sensors described in some embodiments will be able to detect lactulose at a concentration of approximately 0.1 mM or more.

Compositions, Kits, Methods and Uses

The sensors described herein may be included in compositions for use in detecting carbohydrates. For example, the sensors described herein may be included in compositions for use in detecting sugars or sugar derivatives. In one embodiment, the sensors described herein may be included in compositions for use in detecting lactose. In one embodiment, the sensors described herein may be included in compositions for use in detecting lactulose. In some embodiments, there is provided a composition comprising a sensor in accordance with the present invention and an acceptable carrier. As used herein, the term “acceptable carrier” includes any and all solids or solvents (such as phosphate buffered saline buffers, water, saline) dispersion media, coatings, and the like, compatible with the methods and uses of the present invention. The acceptable carriers must be ‘acceptable’ in the sense of being compatible with the other ingredients of the composition, not damaging the carbohydrates being tested for and not inhibiting binding of the carbohydrate to the carbohydrate binding domain. Generally, suitable acceptable carriers are known in the art and are selected based on the end use application.

As the skilled person would appreciate, the sensors of the present application can be used to detect the presence or absence of a carbohydrate in a sample, and if present may also be used to determine the amount of the carbohydrate present in the sample. Therefore, in some embodiments there is provided a method of detecting a carbohydrate in a sample, the method comprising i) contacting a sample with the sensor molecule of the present invention; and ii) determining if the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain has been altered in the presence of the sample, wherein an alteration of the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain indicates the carbohydrate is present in the sample. In some embodiments, determining if the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain has been altered in the presence of the sample comprises measuring the BRET ratio before and after addition of the sample.

In some embodiments, the method further comprises determining the concentration of the carbohydrate in the sample.

In some embodiments, the carbohydrate is selected from the group consisting of lactose and lactulose. In some embodiments, the carbohydrate is lactose. In some embodiments, the carbohydrate is lactulose.

The sensors can be used to detect and quantify carbohydrates in a sample. The “sample” can be any substance or composition that has the potential to contain a carbohydrate. In some embodiments, the sample is air, liquid, biological material or soil. In some embodiments, the sample is selected from the group consisting of a dairy product or an extract thereof, soil or an extract thereof, biological materials or an extract thereof and the like. The sample may be obtained directly from the environment or source, or may be extracted and/or at least partially purified by a suitable procedure before a method of the invention is performed.

In some examples, the sample comprises a biological material. As used herein, “biological materials” is defined broadly and includes any material derived in whole or in part from an organism. Biological materials include, but are not limited to, bodily fluids, cells, soft tissues (such as connective and non-connective tissue) and hard tissues (such as bone and cartilage). In some embodiments, the bodily fluids are blood, serum, sputum, mucus, pus, peritoneal fluid, urine or other bodily fluids. In some embodiments, such materials may have been harvested from a living organism and then subjected to further processing and/or chemical treatment. In an embodiment, the sensor is not used to detect a carbohydrate within a living cell. In some embodiments, the sensor is used ex vivo.

In some examples, the sample comprises a dairy product. As used herein, the term “dairy product” includes milk and products derived partially or in full from milk. The milk may be obtained from any mammal, for example cow, sheep, goat, horse, camel, buffalo, human and the like. Dairy products include, but are not limited to, raw milk, low fat milk, skim milk, pasteurized milk, extended shelf life milk, UHT milk, lactose-modified UHT milk, fortified UHT milk, flavoured UHT milk, and combinations of these products as well as UHT infant formula, cheese, yoghurt, whey, buttermilk, cream, milk powder, powdered infant formula, ice-cream and butter and the like. In some examples, the sample is milk or diluted milk. The dairy product may also be an extract, such as a partially purified portion, of dairy product comprising, or suspected of comprising, the carbohydrate of interest.

In some embodiments, the sensors of the present invention can be used to detect lactose in a dairy product. Accordingly, there is provided a method of detecting lactose in a dairy product, the method comprising i) contacting a sample with the sensor molecule of the present invention; and ii) determining if the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain has been altered in the presence of the sample, wherein an alteration of the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain indicates that lactose is present in the sample.

The sensors of the present invention can also be used to monitor the concentrations of carbohydrate in a sample.

In some embodiments, the sensors of the present invention can be used to detect lactulose in a dairy product. Accordingly, there is provided a method of detecting lactulose in a dairy product, the method comprising i) contacting a sample with the sensor molecule of the present invention; and ii) determining if the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain has been altered in the presence of the sample, wherein an alteration of the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain indicates that lactulose is present in the sample. In some embodiments, the method further comprises determining the concentration of lactulose in the sample.

Lactulose has been proposed by the International Dairy Federation and the European Union as an indicator of milk damage caused by heat-treatment and as a criterion to distinguish between pasteurized milk ([lactulose]<10 μM), ultra-high temperature (UHT)-treated milk ([lactulose]<1.8 mM) and in-container sterilized milk ([lactulose]>1.8 mM) (Marconi et al., 2004; Montilla et al., 1996). In some embodiments, the sensors of the present invention can be used to monitor the concentrations of lactulose in a sample. In some embodiments, the sensors of the present invention can be used to provide an indication of milk damage caused by heat-treatment. In some embodiments, the sensors of the present invention can be used to distinguish between various forms of milk, such as pasteurized milk, ultra-high temperature (UHT)-treated milk and in-container sterilized milk.

In some embodiments, there is also provided use of a sensor molecule for detecting carbohydrate, the sensor molecule comprising:

i) a carbohydrate binding domain of a helix-turn-helix transcription factor, or a variant of the carbohydrate binding domain;

ii) a chemiluminescent donor domain; and

iii) an acceptor domain;

wherein the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain is altered when the carbohydrate binds to the carbohydrate binding domain. In some embodiments, the use further comprises determining the concentration of carbohydrate in the sample.

In some embodiments, there is also provided use of a sensor molecule for detecting lactose, the sensor molecule comprising a bacterial BgaR transcription factor or variant thereof, covalently joined to a resonance energy transfer donor domain and a resonance energy transfer acceptor domain, wherein the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain is altered when lactose binds to the transcription factor. In some embodiments, the use further comprises determining the concentration of lactose in the sample.

In some embodiments, there is also provided use of a sensor molecule for detecting lactulose, the sensor molecule comprising a bacterial BgaR transcription factor or variant thereof, covalently joined to a resonance energy transfer donor domain and a resonance energy transfer acceptor domain, wherein the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain is altered when lactulose binds to the transcription factor. In some embodiments, the use further comprises determining the concentration of lactulose in the sample.

As the skilled person would be aware, the sensors of the present invention can also be multiplexed. In this system, two or more different sensor molecules are provided which detect different carbohydrates. For example, a sensor molecule of the present invention that detects lactose can be multiplexed with sensors that detect other carbohydrates such as lactulose, galactose and/or glucose. In some embodiments, each different sensor molecule may include a different donor and/or acceptor molecule such that they emit at different wavelengths to enable the detection and quantification of different target compounds. In some embodiments, each different sensor molecule may comprise the same donor and/or acceptor molecule. In some embodiments, a single fluidic detection chamber is used. In some embodiments, a multi-channel detection device may be used.

In some embodiments, the sample is an aqueous liquid. For example, the sample includes but is not limited to, milk, fruit juices, other beverages and bodily fluids including blood serum.

The methods of the present invention can be performed on any system suitable for measuring a detectable change.

As the person skilled in the art will appreciate the methods of the present invention can be performed in a batch (for example batch format using a plate reader) or flow format. For example, the methods of the present invention can be performed in a microplate format using a microplate reader equipped with the appropriate filters. The methods of the present invention can also be performed on a microfluidic device, such as described in WO2013/155553.

In another aspect, the present invention provides a kit comprising the sensor as described herein. In some embodiments, the kit further comprises a standard (such as a lactose and/or a lactulose standard).

EXAMPLES Example 1—Construction of LacB1 and LacF1 Sensors

DNA constructs encoding BgaR (codon optimized for expression in E. coli) were synthesised by GenScript (USA). If required, linker sequences were added to the DNA construct by PCR using BgaR synthesised by GenScript as the template and the appropriate primers (Table 5). The primers included the linker sequence (if required) and restriction sites for PstI or BstBI. The amplified PCR product was digested with PstI and BstBI and cloned into pRSET vector (BioLabs, Australia), previously cloned with GFP² and RLuc8 (for the LacB sensors) or CFP and YFP (for the LacF sensors), using the PstI/BstBI restriction sites, such that the expressed fusion protein had an N-terminal histidine tag.

TABLE 5  Oligonucleotides used in the preparation of the  lactose sensors Orientation Sequence P1 Forward AAAAAA CTGCAG ATGCAGATTCTGTG (SEQ ID NO: 10) P2 Reverse ACACAC TTCGAA AATGCTCGGTTTAT (SEQ ID NO: 11) P3 Forward AAAAAA CTGCAG GGTGGTACCGGAGG  CGGCATGCAGATTCTGTGGAAAAA (SEQ ID NO: 12) P4 Reverse AAAAAA TTCGAA GCCGCCTCCGGTA  CCACCAATGCTCGGTTTATTAACTT (SEQ ID NO: 13) P5 Reverse AAAAAA CTGCAG AATGCTCGGTTTAT (SEQ ID NO: 14)

Cells of Escherichia coli strain BL21(DE3) (New England BioLabs) were transformed with pRSET vector encoding the sensor. The sensors were expressed in E. coli strain BL21(DE3) using protocols known to the person skilled in the art.

For expression of the sensors, 50 mL of LB (10 g tryptone, 5 g yeast extract, 5 g NaCl per L of water (pH 7.4)) supplemented with 2% (v/v) glucose and 100 μg/mL ampicillin was inoculated with a single colony and incubated at 37° C., 200 rpm until it reached an Abs₆₀₀ nm of 0.8. 250 mL LB, supplemented with 100 μg/mL ampicillin, was inoculated using the starter culture to an Abs₆₀₀ nm of 0.05 and incubated at 28° C., 200 rpm for 16 hours and the cells were harvested.

Alternatively, 200 mL LB containing 100 μg/mL ampicillin was inoculated with a single colony and the culture was incubated at 28° C. for 48 h with shaking at 200 rpm and the cells were harvested.

Cells were harvested by centrifugation at 5000×g (4° C.) for 10 minutes, washed with phosphate buffered saline (PBS; 137 mM NaCl, 2.7 mM KCl, 10 mM Na₂HPO₄, 1.8 mM KH₂PO₄, pH 7.4) and resuspended in sodium phosphate buffer (50 mM Na₂HPO₄, 300 mM NaCl, pH 7.0). The cells suspension was passed through a homogenizer (Microfluidics M-110P (Newton, Mass., USA)) at a pressure of 20,000 psi and the soluble protein fraction was isolated by centrifugation at 15,000×g (4° C.) for 15 minutes. Proteins were purified using cobalt affinity chromatography (TALON® Superflow Metal Affinity Resin (Takara Clontech, Australia)) according to the manufacturer's instructions. Following elution of the purified protein with 150 mM imidazole, the sample was dialysed against Tris buffer (50 mM Tris, 100 mM NaCl, 0.1 mM EDTA, pH 8.0) using a dialysis unit (GE Healthcare, Vivaspin 6, 10 kDa MWCO). Aliquots of 500 μL of the purified protein were snap-frozen in liquid nitrogen and stored at −80° C. Protein concentrations were determined by absorbance at 280 nm.

The purified LacB1 sensor is a polypeptide having the sequence SEQ ID NO: 15. The LacB1 sensor contains GFP2-BgaR-RLuc8. The purified LacF1 sensor is a polypeptide having the sequence SEQ ID NO: 23. The LacF1 sensor contains CFP-BgaR-YFP. A schematic of the His tagged LacB1 and LacF1 sensors is shown in FIG. 2.

Example 2—Lactose Binding by LacB1 and LacF1 Materials and Methods

BRET assays were carried out in 96-well plates with a final volume of 100 μL. The purified sensor and lactose were diluted to the desired concentration using PBS (58 mM Na₂H₂PO₄, 17 mM NaH₂PO₄, 68 mM NaCl, pH 7.4). The LacB1 sensor was incubated for 5 minutes at 30° C. with 1 mM lactose or water. At the end of the incubation time, 5 μL of coelenterazine 400a in EtOH was added (to a final coelenterazine 400a concentration of 17 μM) and the spectral scans were recorded immediately.

FRET measurements were carried out in a similar manner to the BRET² assays, with the following modifications. The LacF1 sensor was incubated for 5 minutes at 30° C. with 1 mM lactose. Spectral scans were recorded in fluorescence mode (λ_(ex)=435 nm, 455 nm cut-off, 20 nm increments).

Spectral scans were recorded with a SpectraMax M3 plate-reading spectrofluorimeter (Molecular Devices) in luminescence mode (20 nm increments) in white 96-well plates (Opti-Plate™-96, PerkinElmer).

Data Analysis

BRET² ratio was calculated as the ratio of acceptor emission intensity at 500 nm to donor emission intensity at 420 nm.

FRET ratio was calculated as the ratio of acceptor emission intensity at 520 nm to donor emission intensity at 480 nm.

Results

RET ratios were measured for both the LacB1 sensor and the LacF1 sensor in the presence of water or 1 mM lactose (FIG. 2). For both sensors, the presence of 1 mM lactose resulted in a decrease in the RET ratio. For LacB1 the change was from 1.09±0.01 to 0.800±0.003. For LacF1, the change was from 1.216±0.004 to 1.089±0.004. Therefore 1 mM lactose caused a 27% drop in the RET ratio for the LacB1 sensor compared with a 10% decrease for LacF1 sensor.

Example 3—BRET Assays for Detecting Lactose Binding by LacB1 Materials and Methods

BRET assays were carried out in 96-well plates with a final volume of 100 μL. The purified sensor and lactose were diluted to the desired concentration using PBS (58 mM Na₂H₂PO₄, 17 mM NaH₂PO₄, 68 mM NaCl, pH 7.4). Purified sensor (1 μM) was incubated for 30 minutes at 30° C. with varying amounts of lactose (0.000036%-0.36% w/v) or other carbohydrate. For BRET measurement, 5 μL coelenterazine 400a substrate (final [coel 400a]=16.7 μM)) was added following the incubation period. Spectral scans were recorded immediately after the addition of the substrate. Spectral scans were recorded with a Spectramax M2 plate-reading spectrofluorimeter (Molecular Devices).

Data Analysis

BRET² ratios were calculated as the ratio of the maximum acceptor emission intensity (500 nm) to maximum donor emission intensity (420 nm).

Results

The BRET² ratio for the LacB1 sensor in the presence of increasing amounts of lactose is shown in FIG. 3.

Example 4—the Effect of Linker Length on Lactose Binding Materials and Methods

To investigate the effect varying the length of the linker connecting the carbohydrate binding domain to the chemiluminescent donor domain and/or acceptor domain, lactose sensors were constructed in which the linker sequence -GGTGGG- was included before and after BgaR (LacB2; SEQ ID NO: 16), before BgaR (LacB3; SEQ ID NO: 17) and after BgaR (LacB4; SEQ ID NO: 18). The LacB2 sensor contains RLuc8-GGTGGG-BgaR-GGTGGG-GFP². The LacB3 sensor contains RLuc8-GGTGGG-BgaR-GFP². The LacB4 sensor contains RLuc8-BgaR-GGTGGG-GFP². A schematic representation of the lactose sensors is shown in FIG. 4. The linker location is indicated by a darkened section compared to the same area of LacB1. Binding of these sensors to 1 mM lactose was assessed using the BRET assay described in Example 3.

Results

The BRET² ratio for the LacB2, LacB3 and LacB4 sensors in the presence and absence of 1 mM lactose is shown in FIG. 5. The BRET² ratio for the LacB1 sensor in the presence and absence of 1 mM Lactose is included as a comparison. While all sensors exhibited a change in the BRET² ratio in the presence of 1 mM Lactose, LacB1 (no linkers) gave the most substantial change in BRET² ratio in the presence of 1 mM lactose.

Example 5—Sensitivity of the LacB1 and LacF1 Sensors

The process used to generate lactose-free and lactose reduced milk uses β galactosidase (also referred to as lactase) to break the disaccharide lactose into its two component monosaccharides, galactose and glucose. Galactose and glucose remain in the final milk product in high concentrations. Due to their structural similarities with lactose, galactose and glucose have the potential to competitively bind to a lactose biosensor, interfering with the measurement of trace levels of lactose. In addition, the heat treatment of milk to yield long-life product (such as UHT or milk powder, but not pasteurised ‘fresh’ milk) results in partial isomerization of the disaccharide lactose to lactulose. Typically levels of lactulose reach 0.32 to 2.16 mM (0.011 to 0.074% (w/v)) in UHT milk (Morales et al., 2000; Marconi et al., 2004). Lactulose is not hydrolysed to its component monosaccharides by β-galactosidase treatment. Similarly to the monosaccharides galactose and glucose, the presence of lactulose in heat treated milk has the potential to interfere with measurement of low levels of lactose in dairy products.

Materials and Methods

In order to determine whether the LacB1 sensor has sufficient specificity and sensitivity to avoid interference by sugars such as galactose, glucose and lactulose, the ability of the LacB1 sensor to bind a range of disaccharides that are structurally related to lactose (β-D-galactosyl-(1→4)-D-glucose), namely lactulose (4-O-β-D-galactosyl-D-fructose), melibiose (D-galactosyl-α(1→6)-D-glucose), maltose (4-O-α-D-glucosyl-D-glucose), cellobiose (4-O-β-D-glucosyl-D-glucose), trehalose (α-D-glucosyl-(1→1)-α-D-glucose) and sucrose (β-D-Fructosyl α-D-glucose), as well as the monosaccharides, galactose and glucose was assessed using the BRET assay described in Examples 2 and 3.

Briefly, the LacB1 sensor was incubated separately with 0.1 mM or 1 mM lactose, 1 mM lactulose, melibiose, maltose, cellobiose, trehalose or sucrose or 1 mM or 10 mM galactose or glucose.

Next, a ‘corrected’ calibration curve for the LacB1 and LacF1 sensors in the presence of glucose and galactose was generated following the protocol detailed in Example 3, however to simulate a 1 in 10 dilution of treated milk in phosphate buffer saline (PBS) glucose and galactose were included at a concentration such that [lactose]+0.5×[galactose]+0.5×[glucose]=13.9 mM and [galactose]=[glucose]. For example, if 139 mM of lactose is found in milk prior to treatment by lactase, following lactase treatment to a residual [lactose] of 1 mM, galactose and glucose would be present at concentrations of 138 mM. In the case of a 1 in 10 dilution of such a lactase treated milk sample in PBS, the diluted sample would contain 0.1 mM of residual lactose and 13.8 mM of both galactose and glucose. Therefore, when the reaction mix contained 0.1 mM lactose, 13.8 mM glucose and 13.8 mM galactose were also added.

A ‘corrected’ calibration curve was also constructed for the LacB1 and LacF1 sensors in the presence of glucose and galactose using lactose-free full fat milk which had been dialysed to remove low molecular weight components, particularly lactose, galactose and glucose, as the diluent. To remove, full cream lactose-free milk was dialysed according to the following protocol. 10 mL of lactose-free full-fat milk was dialysed twice against 1000 mL PBS at 4° C. for 24 h to remove any residual lactose present in lactose-free milk. 1 mL aliquots of the dialysed milk were frozen on dry ice and stored at −80° C. The dialysed milk was used as the ‘milk matrix’ at a 1 in 10 dilution in PBS.

Results and Discussion

The changes in BRET² ratio for the LacB1 sensor in the presence of lactose, lactulose, melibiose, maltose, cellobiose, trehalose, sucrose, galactose and glucose for 30 minutes is shown in FIG. 6.

Incubation of the LacB1 sensor with 1 mM (0.034% w/v) of the disaccharide lactulose resulted in a change in BRET² ratio of approximately 21%, whereas the other disaccharides led to BRET² ratio changes between 3 and 10%. In comparison, the change in BRET² ratio upon the addition of 1 mM (0.034%) lactose was approximately 35%. This indicates that the LacB1 sensor is selective for lactose over other saccharides.

Incubation of the LacB1 sensor with 1 and 10 mM (0.018% and 0.18%) galactose or glucose resulted in 3 and 13% changes in the BRET² ratios with the galactose and 9 and 6% changes with the glucose.

Similar results were obtained when the LacB1 sensor was incubated in the presence of lactose, lactulose, melibiose, maltose, cellobiose, trehalose, sucrose, galactose and glucose for 5 minutes before coelenterazine 400a was added (FIG. 7).

Corrected calibration curves for the LacB1 and LacF1 sensors in PBS and 10% dialysed milk in PBS are shown in FIG. 8. FIGS. 8A and 8B shows the corrected calibration curves in PBS. FIGS. 8C, 8D and 8E shows the corrected calibration curves in 10% dialysed milk in PBS. The corrected calibration curves are linear over at least 2 log units to allow lactose quantification. Samples with higher lactose content can be analysed using the same method by diluting the sampling 10:90 with buffer (see FIG. 8).

Example 6—LacB1 Binding to Lactose and Lactulose

Of the sugars tested in Example 5, lactose caused the largest change in BRET² ratio, followed by lactulose. Since LacB1 exhibited the largest responses to lactose and lactulose, the affinity of the biosensor for each respective sugar was investigated further.

Materials and Methods

Spectral scans were recorded with a SpectraMax M3 plate-reading spectrofluorimeter (Molecular Devices) in luminescence mode (20 nm increments) in white 96-well plates (Opti-Plate™-96, PerkinElmer). 1 μM of purified protein was used for the BRET assay, in a final volume of 100 μL, where the protein and analyte were diluted in phosphate-buffered saline (PBS; 10 mM phosphate, 137 mM NaCl, 2.7 mM KCl, pH 7.3) or 10% (v/v) dialysed lactose-free, full cream milk in PBS. The purified protein was incubated for 5 minutes at 30° C. with lactose or lactulose. At the end of the incubation time, 5 μL of coelenterazine 400a in EtOH was added (to a final coelenterazine 400a concentration of 17 μM) and the spectral scans were recorded immediately.

Data Analysis

BRET² ratio was calculated as the ratio of acceptor emission intensity at 500 nm to donor emission intensity at 420 nm.

Results and Discussion

The changes in BRET² ratio for the LacB1 sensor in the presence of lactose or lactulose is shown in FIG. 9. The response of LacB1 to lactose and lactulose (in PBS) was concentration dependent. The response of LacB1 to lactose was quasi-linear over almost 3 log units with an EC₅₀ of 12±1 μM and a limit of detection of 1 μM. The affinity of LacB1 for lactulose was approximately 150 fold weaker, with an EC₅₀ of 2.4±0.2 mM. The limit of detection for lactulose was 0.1 mM i.e. 100 fold higher than for lactose. The lactulose response was quasi-linear over almost 2 log units. The limit of detection of LacB1 for lactulose (0.1 mM) is 10-fold higher than the lactulose levels found in pasteurized milk (10 μM), which means it could be used to determine any relevant level of lactose in lactase treated pasteurized milk.

The response of the LacB1 sensor to lactose in 10% (v/v) dialysed milk is concentration dependent with an EC₅₀ of 21±2 μM, linearity over almost 3 log units and a limit of detection of 1 μM. The sensitivity of LacB1 to lactose in 10% (v/v) dialysed milk and saturating concentrations of galactose and glucose is statistically different from that observed in PBS only (11-14 μM & 18-23 μM). However, the affinity of LacB1 for lactose was not decreased dramatically by the presence of either 10% (v/v) dialysed milk or high concentrations of glucose and galactose. Without wishing to be bound by theory, it is thought that this is due to the high selectivity of the sensor for lactose and/or due to the efficiency of the BRET² transduction mechanism in complex media.

The characterization of LacB1 binding with lactose and lactulose highlights the intrinsic power of using binding proteins as analyte recognition elements for biosensing, particularly when coupled with the BRET² transduction mechanism for detecting the change. The lactose binding transcriptional regulator, BgaR, used to construct LacB1 yielded sensitivity in the low micromolar range, with the ability to discriminate between structurally related disaccharides, as demonstrated by the 200-fold difference in EC₅₀ observed between lactose and the second most potent sugar tested, lactulose.

Example 7—LacB1 Binding to Lactose in a Simulated Milk System

To investigate the effects of measuring the lactose concentrations in a simulated milk system, a dialysed milk sample was used where the total concentration of sugars was held constant by adding compensating amounts of glucose and galactose as the lactose concentration was reduced from 13.9 mM (equivalent to unmodified 10% (v/v) whole milk) to zero.

Materials and Methods

Full cream milk was dialysed against water to eliminate small molecules. Briefly, 20 mL of full cream lactose-free milk was dialysed twice against 1 L of water at 4° C. for 90 minutes in a D-Tube™ Dialyzer (Merck, 3.5 kDa MWCO). 1 mL aliquots of the dialysed milk were frozen on dry ice and stored at −80° C.

The dialysed milk was used to reconstitute a 10% (v/v) milk matrix with a range of precisely defined levels of lactose, galactose and glucose where ([lactose]+[galactose+glucose]/2=13.9 mM. The ten-fold dilution factor was chosen to accurately simulate assay conditions when measuring lactose in samples at or below the 300 μM ‘lactose-free’ threshold, i.e. following lactase treatment. The BRET assays was performed as described in Example 6.

Results and Discussion

The changes in BRET² ratio for the LacB1 sensor in a simulated milk system is shown in FIG. 9. Under these conditions, which closely mimic the situation in milk samples, the LOD for lactose was 0.2 μM (0.00003% w/v). The EC₅₀ for lactose changed marginally under these conditions, from 12 to 21 μM, but the difference was not statistically different. The EC₅₀ for lactose is approximately 15 fold lower than the most stringent objective regulatory standard (0.01% w/v) for “lactose free” dairy products. The similarity of the log concentration-response functions in the presence or absence of 10% (w/v) full cream milk is remarkable because in the latter case, at lower concentrations of lactose, the measurements are made in the presence of 13.9 mM glucose and galactose. Without wishing to be bound by theory, it is thought that the strong ability of the biosensor to “ignore” potentially interfering substances arises from the selectivity of the sensor, the robust ratiometric nature of the BRET² transduction mechanism and/or the absence of an external source of illumination, which would cause light scattering and increase noise in a turbid medium such as milk, even when diluted tenfold.

Example 8—CYBERTONGUE® Assay for Lactose Materials and Methods

LacB1 was diluted to 1200 μM in assay buffer (0.45% gelatine in phosphate buffer saline: 0.45% (w/v) gelatine from fresh water fish skin (Sigma Aldrich), 58 mM Na₂H₂PO₄, 17 mM NaH₂PO₄, 68 mM NaCl, pH 7.4). 35 μL of analyte (30 μM or 3 mM lactose in assay buffer or assay buffer alone), LacB1 (1200 μM) and coelenterazine 400a (30 μM in 15% EtOH/assay buffer) were placed one in each of the three inlets of the CYBERTONGUE® microfluidic chip and the assay was performed at a flow rate of 1200 μL/h for 100 sec.

BRET ratios were recorded using the CYBERTONGUE® device with a flow rate of 1200 μL/h and the donor and acceptor luminescence intensities averaged between 80 and 100 sec. BRET² ratios were calculated by the CYBERTONGUE® device software program as the ratio of the maximum acceptor emission intensity (green filter) to maximum donor emission intensity (blue filter).

Results

An example CYBERTONGUE® device trace for assay buffer with 3 mM lactose is shown in FIG. 10. As is shown in FIG. 11, the CYBERTONGUE® assay can be used to detect lactose at both 30 μM and 3 mM. The addition of 30 μM and 3 mM lactose resulted in approximately 22% and 41% changes in the BRET² ratios, respectively.

Example 9—Estimation of Lactose in Whole Milk

Engineering a sensor to quantify an analyte in a defined buffer under controlled laboratory conditions is of itself a challenge but accurately quantifying an analyte under real world conditions is even more challenging. In particular, complex and interfering sample matrices, such as milk, dairy and other biological samples, can complicate and 10 degrade biosensor performance. One use of the sensors described herein would be to quantify lactose levels, which range from approximately 4.5 to 7.0% (w/v), depending on species, in unmodified milk. The present inventors compared the lactose estimates obtained with using the sensor described herein, calibrated against known amounts of lactose in PBS or 10% of a dialysed milk matrix with two methods currently in commercial use, a coupled-enzyme lactose assay kit (BioVision) and HPLC with refractive index detector performed in a NATA accredited analytical laboratory.

Materials and Methods

The concentration of lactose in whole milk was estimated using a commercial kit (The BioVision lactose colorimetric/fluorometric assay kit (San Francisco, USA, # K624-100)), by HPLC with refractive index (RI) detection and using the LacB1 sensor described herein.

The sample used in these assays was whole pasteurized cow's milk purchased from a supermarket. The nutritional panel on the carton of milk stated a representative value for lactose of 137 mM.

The BioVision lactose colorimetric/fluorometric assay kit was used in accordance with the manufacturer's instructions to estimate lactose and galactose concentration. Briefly, a standard curve was prepared using 0, 2, 4, 6, 8 or 10 μL of a lactose standard (1 mM in the provided lactose assay buffer). The required volume was pipetted into individual wells of a clear 96-well plate (UV-star microplate, Greiner). Whole pasteurized cow's milk purchased was diluted approximately 10⁴ fold in water and 10 μL was used for the assay. In addition, 2 μL of the chromogenic probe, 2 μL of enzyme mix, and 2 μL of horseradish oxidase (HRP) were added to each well and volumes were made up to 100 μL with lactose assay buffer and mixed well. The reaction mixtures were incubated at 37° C. for 60 minutes and protected from light. Abs_(570nm) was recorded with a SpectraMax M3 plate-reading spectrofluorimeter (Molecular Devices) in the absorbance mode (end-point measurement Abs_(570 nm)). The assay was performed in triplicate.

HPLC estimation of lactose concentration was performed by a commercial laboratory. Briefly, 200 mL of whole milk was frozen and stored at −80° C. and shipped on dry ice to a commercial NATA-accredited testing laboratory (DTS/Asure Quality, Melbourne, Australia). Analysis was performed according to the laboratory's standard commercial protocol, using HPLC and RI detection (Chaves-Servin et al., 2004; Southgate, 1969). Results were reported as g of sugar per 100 mL of milk, using 1.033 g/mL as the density of full cream whole milk. No error values were reported.

Estimation of lactose concentration was performed using the LacB1 sensor, calibrated against known amounts of lactose in PBS or 10% of a dialysed milk matrix, as described herein. The EC₅₀ of LacB1 for lactose is 12 μM, i.e. approximately 10⁴-fold lower than the lactose concentration found in unmodified cow's milk. Consequently, whole milk samples were diluted 3200 fold in water prior to lactose estimation.

Results

The lactose concentration of pasteurized whole cow's determined using the LacB1 sensor, the BioVision kit and HPLC is presented in Table 6.

Using the BioVision coupled-enzyme kit and following the manufacturer's protocol the inventors estimated the lactose concentration of the whole milk sample to be 129±1 mM.

A sample of the same milk was submitted to a NATA accredited laboratory for lactose estimation by HPLC/refractive index (RI) analysis. The laboratory reported a lactose concentration of 134 mM. In this case, no error value was reported.

Using the LacB1 sensor as described herein the inventors estimated that the lactose concentration in the whole milk sample was 157±6 mM.

TABLE 6 Comparison of lactose concentration in pasteurized whole cow's determined using the LacB1 sensor and two independent methods. [Lactose] [Lactose] (mM) (% w/v) LacB1 sensor 157 ± 6 5.4 ± 0.2  Coupled enzyme 129 ± 1 4.4 ± 0.03 assay (BioVision) HPLC with RI 134* 4.6 detection*

Example 10—Estimation of Lactose in Lactase-Treated Milk

A further use of a lactose biosensor is to measure lactose in different grades of lactase treated milk, characterized as “reduced lactose” or “lactose-free”. Estimation of lactose in lactase-treated milk is challenging due to the low level of the analyte, the complexity of the milk medium and the presence of high levels of glucose and galactose that can interfere with the measurement of lactose itself. Food Standards Australia and New Zealand (FSANZ) specifies lactose-reduced dairy as containing no more than 0.3% (8.8 mM) lactose whereas lactose-free products should contain “no detectable lactose”, a subjective, method-dependent definition. European authorities specify an objective threshold for lactose-free foods at 0.01% (w/v) (0.3 mM).

Milk is a complex matrix comprising proteins and lipids each at concentrations of approximately 3% (w/v) (Kailasapathy, 2009). To minimize interference, analytical laboratories routinely precipitate fats and proteins from milk samples before analyzing the sugar content by HPLC or colorimetric coupled-enzyme assays. In addition to being time consuming and incurring extra cost, work-up of samples prior to analysis increases the risk of error due to yield variation and modification of sample volumes. There is a need for an improved method of determining the concentration of a carbohydrate, for example lactose, in a sample that avoids at least some of the disadvantages associated with HPLC or colorimetric coupled-enzyme assays.

Materials and Methods

The concentration of lactose in commercially obtained full cream, “lactose-free” cow's milk was estimated using a commercial kit (The BioVision lactose colorimetric/fluorometric assay kit (San Francisco, USA, # K624-100)), by HPLC with refractive index (RI) detection and using the LacB1 sensor as described for Example 9.

The sample used in these assays was commercially obtained full cream, “lactose-free” cow's milk. A ten-fold dilution of the “lactose-free” cow's milk was used for the LacB1 assay.

The concentration of galactose in the sample was also determined using the commercial kit (The BioVision lactose colorimetric/fluorometric assay kit (San Francisco, USA, # K624-100)) and by HPLC with refractive index (RI) detection using standard protocols.

Results

The LacB1 sensor was used to estimate lactose concentration in a ten-fold dilution of commercially obtained full cream, “lactose-free” cow's milk. The BRET² ratio was decreased by 16%, equivalent to a concentration of 2.7±0.1 μM, corresponding to 27±1 μM lactose in the original milk sample (Table 7).

Attempts to estimate the lactose concentration of full cream, “lactose-free” cow's milk using the BioVision lactose colorimetric/fluorometric assay kit described in Example 9 were unsuccessful. It was thought that this was a result of the high concentrations of galactose present in the “lactose-free” cow's milk. The concentration of galactose in the sample was estimated to be 163±2 mM.

Samples of the same full cream, lactose-free milk were submitted to a NATA accredited analytical laboratory for analysis by HPLC-refractive index detection. No lactose was detected, with a limit of detection of 0.1% (w/v) or approximately 3 mM (Table 7).

TABLE 7 Comparison of lactose concentration in fresh “lactose free” full cream cow's milk using the LacB1 sensor and two independent methods. [Lactose] [Lactose] [Galactose] (mM) (% w/v) (mM) LacB1 sensor 0.027 ± 0.001 0.00092 ± 0.00003 NA Coupled enzyme NA NA 163 ± 2 assay (BioVision) HPLC with RI <3 <0.1 124 detection* *No error quoted

Therefore, the LacB1 sensor appears to be suitable for directly determining the concentration of residual lactose in lactose free commercial dairy products.

This application claims priority from Australian application no. 2017903148 filed 8 Aug. 2017, the entire contents of which are incorporated by reference herein.

It will be appreciated by persons skilled in the art that numerous variations and/or modifications may be made to the invention as shown in the specific embodiments without departing from the spirit or scope of the invention as broadly described. The present embodiments are, therefore, to be considered in all respects as illustrative and not restrictive.

All publications discussed and/or referenced herein are incorporated herein in their entirety.

Any discussion of documents, acts, materials, devices, articles or the like which has been included in the present specification is solely for the purpose of providing a context for the present invention. It is not to be taken as an admission that any or all of these matters form part of the prior art base or were common general knowledge in the field relevant to the present invention as it existed before the priority date of each claim of this application.

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1. A sensor molecule for detecting a carbohydrate, the sensor comprising i) a carbohydrate binding domain of a helix-turn-helix transcription factor, or a variant of the carbohydrate binding domain; ii) a chemiluminescent donor domain; and iii) an acceptor domain; wherein the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain is altered when the carbohydrate binds to the carbohydrate binding domain.
 2. The sensor molecule of claim 1, wherein the helix-turn-helix transcription factor is a bacterial helix-turn-helix transcription factor, or a variant thereof.
 3. The sensor molecule of claim 1 or claim 2, wherein the bacterial helix-turn-helix transcription factor is a G_(NT)R transcription factor, or a variant thereof.
 4. The sensor molecule of any one of claims 1 to 3, wherein the bacterial helix-turn-helix transcription factor or variant thereof, has an amino acid sequence which is at least 30% identical to that provided in any one or more of SEQ ID NO's 9 and 56 to
 74. 5. The sensor molecule according to any one of claims 1 to 4, wherein the carbohydrate is a sugar or sugar derivative.
 6. The sensor molecule of claim 5 wherein the sugar is a disaccharide.
 7. The sensor molecule of claim 6, wherein the disaccharide is lactose.
 8. The sensor molecule according to claim 5, wherein the sugar derivative is selected from the group consisting of amino sugars, acidic sugars, deoxy sugars, sugar alcohols, glycosylamines and sugar phosphates.
 9. The sensor molecule according to any one of claims 1 to 8, wherein the chemiluminescent donor domain is a bioluminescent protein.
 10. The sensor molecule of claim 9, wherein the bioluminescent protein is a luciferase, a β-galactosidase, a lactamase, a horseradish peroxidase, an alkaline phosphatase, α-glucuronidase or α-glucosidase.
 11. The sensor molecule of claim 10, wherein the luciferase is a Renilla luciferase, a Firefly luciferase, a Coelenterate luciferase, a North American glow worm luciferase, a click beetle luciferase, a railroad worm luciferase, a bacterial luciferase, a Gaussia luciferase, Aequorin, an Arachnocampa luciferase, an Oplophorus gracilirostris luciferase or a biologically active variant or fragment of any one, or chimera of two or more, thereof.
 12. The sensor molecule according to any one of claims 1 to 11, wherein the chemiluminescent donor domain is capable of modifying a substrate.
 13. The sensor molecule of claim 12, wherein the substrate is luciferin, calcium, coelenterazine, furimazine or a derivative, analogue or stabilised derivative of coelenterazine, luciferin or furimazine.
 14. The sensor molecule according to any one of claims 1 to 13, wherein the acceptor domain is a fluorescent acceptor domain.
 15. The sensor molecule of claim 14, wherein the fluorescent acceptor domain is selected from the group consisting of green fluorescent protein (GFP), blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Venus, mOrange, Topaz, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), HcRed, t-HcRed, DsRed, DsRed2, t-dimer2, tdimer2(12), mRFP1, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein, tdTomato, mCherry, TagRFP, TurBoFB and a Phycobiliprotein, and a biologically active variant or fragment of any one thereof.
 16. The sensor molecule according to any one of claims 1 to 15, wherein the separation and relative orientation of the chemiluminescent donor domain and the acceptor domain, in the presence and/or the absence of carbohydrate, is within ±50% of the Förster distance.
 17. The sensor molecule of claim 16, wherein the Förster distance of the chemiluminescent donor domain and the acceptor domain is at least 5.6 nm.
 18. The sensor molecule of claim 17, wherein the Förster distance of the chemiluminescent donor domain and the acceptor domain is between about 5.6 nm and about 10 nm.
 19. The sensor molecule of any one of claims 1 to 18 which is a single polypeptide.
 20. The sensor molecule of claim 19, wherein the chemiluminescent donor domain is at the N-terminus and the acceptor domain is at the C-terminus.
 21. The sensor molecule of claim 19, wherein the acceptor domain is at the N-terminus and the chemiluminescent donor domain is at the C-terminus.
 22. The sensor molecule according to any one of claims 19 to 21 which comprises at least one peptide linker.
 23. A method of detecting a carbohydrate in a sample, the method comprising i) contacting a sample with the sensor molecule of any one of claims 1 to 22; and ii) determining if the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain has been altered in the presence of the sample, wherein an alteration of the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain indicates the carbohydrate is present in the sample.
 24. The method of claim 23 which further comprises determining the concentration of the carbohydrate in the sample.
 25. The method of claim 23 or claim 24 which is performed on a microfluidic device.
 26. The method according to any one of claims 23 to 25, wherein the sample is air, liquid, biological material or soil.
 27. The method according to any one of claims 23 to 26, wherein the sample comprises a dairy product.
 28. The method of claim 27, wherein the sample is milk.
 29. A polynucleotide encoding a sensor molecule according to any one of claims 19 to
 22. 30. A vector comprising the polynucleotide of claim
 29. 31. A host cell comprising the polynucleotide of claim 29 and/or the vector of claim
 30. 32. A process for producing a sensor molecule, the process comprising cultivating a host cell of claim 31 or a vector of claim 30 under conditions which allow expression of the polynucleotide encoding the polypeptide, and recovering the expressed polypeptide.
 33. A sensor molecule for detecting lactose comprising a bacterial BgaR transcription factor or variant thereof, covalently joined to a resonance energy transfer donor domain and a resonance energy transfer acceptor domain, wherein the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain is altered when lactose binds to the transcription factor.
 34. A sensor molecule for detecting lactulose comprising a bacterial BgaR transcription factor or variant thereof, covalently joined to a resonance energy transfer donor domain and a resonance energy transfer acceptor domain, wherein the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain is altered when lactulose binds to the transcription factor.
 35. The sensor molecule of claim 33 or claim 34, wherein the transcription factor or variant thereof, has an amino acid sequence which is at least 60%, 70%, 80%, 85%, 90%, 95%, 98% or 99% identical to that provided in SEQ ID NO:
 1. 36. The sensor molecule of any one of claims 33 to 35, wherein the resonance energy transfer donor domain is a fluorescent protein.
 37. The sensor molecule of claim 36, wherein the fluorescent protein is selected from the group consisting of green fluorescent protein (GFP), blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Venus, mOrange, Topaz, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), HcRed, t-HcRed, DsRed, DsRed2, t-dimer2, tdimer2(12), mRFP1, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein, tdTomato, mCherry, TagRFP, TurBoFB and a Phycobiliprotein, and a biologically active variant or fragment of any one thereof.
 38. The sensor molecule according to any one of claims 33 to 37, wherein the resonance energy transfer acceptor domain is a fluorescent protein.
 39. The sensor molecule of claim 38, wherein the fluorescent protein is selected from the group consisting of green fluorescent protein (GFP), blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Venus, mOrange, Topaz, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), HcRed, t-HcRed, DsRed, DsRed2, t-dimer2, tdimer2(12), mRFP1, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein, tdTomato, mCherry, TagRFP, TurBoFB and a Phycobiliprotein, and a biologically active variant or fragment of any one thereof.
 40. The sensor molecule of any one of claims 33 to 39, wherein the donor domain is CFP or a variant thereof and the acceptor domain is YFP or a variant thereof.
 41. The sensor molecule of claim 40, having at least 60%, 70%, 80%, 85%, 90%, 95%, 98%, 99% or 100% sequence identity to the polypeptide provided in SEQ ID NO:
 23. 42. A method of detecting lactose in a sample, the method comprising i) contacting a sample with the sensor molecule of any one of claims 33 and 35 to 41; and ii) determining if the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain has been altered in the presence of the sample, wherein an alteration of the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain indicates that lactose is present in the sample.
 43. The method of claim 42, which further comprises determining the concentration of lactose in the sample.
 44. A method of detecting lactulose in a sample, the method comprising i) contacting a sample with the sensor molecule of any one of claims 34 to 41; and ii) determining if the spatial location and/or dipole orientation of the donor domain relative to the acceptor domain has been altered in the presence of the sample, wherein an alteration of the spatial location and/or dipole orientation of the chemiluminescent donor domain relative to the acceptor domain indicates that lactulose is present in the sample.
 45. The method of claim 44, which further comprises determining the concentration of lactulose in the sample.
 46. The method of any one of claims 42 to 45, which is performed on a microfluidic device.
 47. The method according to any one of claims 42 to 46, wherein the sample comprises a dairy product. 